problem installing ENmix package
2
0
Entering edit mode
lea • 0
@lea
Last seen 6 weeks ago

Hello,

I'm trying to install the ENmix package, I used BiocManager::install("ENmix") and it succesfully unpacked. But when I load it with library it says:

Erreur : package or namespace load failed for ‘ENmix’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
no package called ‘rtracklayer’ was found
Also : There were 13 warnings (use warnings() to see them)

I tried loading the package rtracklayer (BiocManager::install("rtracklayer")) and I had the error:

The downloaded source packages are in
‘C:\Users\User\AppData\Local\Temp\Rtmp8Uku7c\downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘rtracklayer’ had non-zero exit status

I tried looking on the internet but I'm a beginner so I don't really get what I should do and some solution where on Linux so I can't try it. Thank you for your help!

sessionInfo( )
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252 
[2] LC_CTYPE=French_France.1252   
[3] LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices
[6] utils     datasets  methods   base     

other attached packages:
 [1] BiocInstaller_1.12.1       
 [2] SummarizedExperiment_1.20.0
 [3] Biobase_2.50.0             
 [4] GenomicRanges_1.42.0       
 [5] GenomeInfoDb_1.26.2        
 [6] IRanges_2.24.1             
 [7] S4Vectors_0.28.1           
 [8] BiocGenerics_0.36.0        
 [9] MatrixGenerics_1.2.1       
[10] matrixStats_0.58.0         
[11] doParallel_1.0.16          
[12] iterators_1.0.13           
[13] foreach_1.5.1              

loaded via a namespace (and not attached):
 [1] bitops_1.0-6             
 [2] bit64_4.0.5              
 [3] RColorBrewer_1.1-2       
 [4] progress_1.2.2           
 [5] httr_1.4.2               
 [6] dynamicTreeCut_1.63-1    
 [7] tools_4.0.2              
 [8] doRNG_1.8.2              
 [9] nor1mix_1.3-0            
[10] utf8_1.1.4               
[11] R6_2.5.0                 
[12] HDF5Array_1.18.1         
[13] DBI_1.1.1                
[14] rhdf5filters_1.2.0       
[15] tidyselect_1.1.0         
[16] prettyunits_1.1.1        
[17] base64_2.0               
[18] curl_4.3                 
[19] bit_4.0.4                
[20] compiler_4.0.2           
[21] preprocessCore_1.52.1    
[22] xml2_1.3.2               
[23] DelayedArray_0.16.2      
[24] RPMM_1.25                
[25] genefilter_1.72.1        
[26] askpass_1.1              
[27] rappdirs_0.3.3           
[28] stringr_1.4.0            
[29] digest_0.6.27            
[30] illuminaio_0.32.0        
[31] siggenes_1.64.0          
[32] XVector_0.30.0           
[33] pkgconfig_2.0.3          
[34] scrime_1.3.5             
[35] sparseMatrixStats_1.2.1  
[36] dbplyr_2.1.0             
[37] fastmap_1.1.0            
[38] limma_3.46.0             
[39] rlang_0.4.10             
[40] rstudioapi_0.13          
[41] RSQLite_2.2.3            
[42] impute_1.64.0            
[43] DelayedMatrixStats_1.12.3
[44] generics_0.1.0           
[45] mclust_5.4.7             
[46] BiocParallel_1.24.1      
[47] dplyr_1.0.4              
[48] RCurl_1.98-1.2           
[49] magrittr_2.0.1           
[50] GenomeInfoDbData_1.2.4   
[51] Matrix_1.3-2             
[52] fansi_0.4.2              
[53] Rcpp_1.0.6               
[54] Rhdf5lib_1.12.1          
[55] lifecycle_1.0.0          
[56] stringi_1.5.3            
[57] MASS_7.3-53.1            
[58] zlibbioc_1.36.0          
[59] BiocFileCache_1.14.0     
[60] rhdf5_2.34.0             
[61] plyr_1.8.6               
[62] grid_4.0.2               
[63] blob_1.2.1               
[64] crayon_1.4.1             
[65] lattice_0.20-41          
[66] Biostrings_2.58.0        
[67] splines_4.0.2            
[68] multtest_2.46.0          
[69] annotate_1.68.0          
[70] hms_1.0.0                
[71] locfit_1.5-9.4           
[72] pillar_1.5.0             
[73] beanplot_1.2             
[74] rngtools_1.5             
[75] geneplotter_1.68.0       
[76] codetools_0.2-18         
[77] biomaRt_2.46.3           
[78] glue_1.4.2               
[79] XML_3.99-0.5             
[80] BiocManager_1.30.10      
[81] vctrs_0.3.6              
[82] purrr_0.3.4              
[83] openssl_1.4.3            
[84] assertthat_0.2.1         
[85] reshape_0.8.8            
[86] cachem_1.0.4             
[87] xfun_0.21                
[88] xtable_1.8-4             
[89] survival_3.2-7           
[90] tibble_3.1.0             
[91] tinytex_0.29             
[92] AnnotationDbi_1.52.0     
[93] memoise_2.0.0            
[94] cluster_2.1.1            
[95] ellipsis_0.3.1
ENmix Bioconductor rtracklayer • 318 views
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0
Entering edit mode
@james-w-macdonald-5106
Last seen 16 hours ago
United States

What you provided was the warning, not the error. There was probably something else in the output that was the actual error, but without that it's hard to help you. Usually there will be something where it says a certain package isn't installed, and you can just go and install that package first and then you will be able to install rtracklayer.

An alternative is to check the validity of your install:

library(BiocManager)
BiocManager::valid()

And if there are any problems it will tell you what to do to fix them.

0
Entering edit mode

Hello, thank for your answer!

You're right I forgot the error message, it says:

C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lzlib1bioc
collect2.exe: error: ld returned 1 exit status
aucune DLL n'a pas été créé
ERROR: compilation failed for package 'rtracklayer'
* removing 'C:/Users/Léa Michel/Documents/R/win-library/4.0/rtracklayer'

I tried to check the validity of the BiocManager package and it says "True" so I guess at leats everything is fine on this part.

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0
Entering edit mode

Does installing zlibbioc help? I can install the source version on Windows, and it makes repeated calls to zlibbioc.

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0
Entering edit mode

No but I'm not sure it even install zlibbioc when I asked since I had this response with a "permission denied" at the end:

BiocManager::install("zlibbioc")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'zlibbioc'
essai de l'URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/zlibbioc_1.36.0.zip'
Content type 'application/zip' length 365125 bytes (356 KB)
downloaded 356 KB

package ‘zlibbioc’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘zlibbioc’
Warning: restored ‘zlibbioc’

The downloaded binary packages are in
    C:\Users\Léa Michel\AppData\Local\Temp\Rtmp8Uku7c\downloaded_packages
Old packages: 'isoband'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
        binary source needs_compilation
isoband  0.2.3  0.2.4              TRUE

installing the source package ‘isoband’

essai de l'URL 'https://cran.rstudio.com/src/contrib/isoband_0.2.4.tar.gz'
Content type 'application/x-gzip' length 2010708 bytes (1.9 MB)
downloaded 1.9 MB

* installing *source* package 'isoband' ...
** package 'isoband' correctement décompressé et sommes MD5 vérifiées
** using staged installation
** libs

*** arch - i386
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c clip-lines.cpp -o clip-lines.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c isoband.cpp -o isoband.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c polygon.cpp -o polygon.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c separate-polygons.cpp -o separate-polygons.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c test-clip-lines.cpp -o test-clip-lines.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o
In file included from test-runner.cpp:8:
testthat/testthat.h: In function 'std::ostream& Catch::cout()':
testthat/testthat.h:145:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
testthat/testthat.h: In function 'std::ostream& Catch::cerr()':
testthat/testthat.h:152:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c test-separate-polygons.cpp -o test-separate-polygons.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o isoband.dll tmp.def clip-lines.o init.o isoband.o polygon.o separate-polygons.o test-clip-lines.o test-runner.o test-separate-polygons.o -LC:/PROGRA~1/R/R-40~1.2/bin/i386 -lR
installing to C:/Users/Léa Michel/Documents/R/win-library/4.0/00LOCK-isoband/00new/isoband/libs/i386

*** arch - x64
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c clip-lines.cpp -o clip-lines.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c isoband.cpp -o isoband.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c polygon.cpp -o polygon.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c separate-polygons.cpp -o separate-polygons.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c test-clip-lines.cpp -o test-clip-lines.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o
In file included from test-runner.cpp:8:
testthat/testthat.h: In function 'std::ostream& Catch::cout()':
testthat/testthat.h:145:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
testthat/testthat.h: In function 'std::ostream& Catch::cerr()':
testthat/testthat.h:152:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -Itestthat         -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c test-separate-polygons.cpp -o test-separate-polygons.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o isoband.dll tmp.def clip-lines.o init.o isoband.o polygon.o separate-polygons.o test-clip-lines.o test-runner.o test-separate-polygons.o -LC:/PROGRA~1/R/R-40~1.2/bin/x64 -lR
installing to C:/Users/Léa Michel/Documents/R/win-library/4.0/00LOCK-isoband/00new/isoband/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'isoband'
    finding HTML links ... fini
    angle_halfcircle_bottom                 html  
    clip_lines                              html  
    iso_to_sfg                              html  
    isoband-package                         html  
    isobands                                html  
    isobands_grob                           html  
    isolines_grob                           html  
    label_placer                            html  
    label_placer_simple                     html  
    plot_iso                                html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (isoband)

The downloaded source packages are in
    ‘C:\Users\Léa Michel\AppData\Local\Temp\Rtmp8Uku7c\downloaded_packages’
Warning message:
In file.copy(savedcopy, lib, recursive = TRUE) :
  problème lors de la copie de C:\Users\Léa Michel\Documents\R\win-library\4.0\00LOCK\zlibbioc\libs\x64\zlib1bioc.dll vers C:\Users\Léa Michel\Documents\R\win-library\4.0\zlibbioc\libs\x64\zlib1bioc.dll: Permission denied
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0
Entering edit mode

Ah, that explains it. When R installs a package, it first creates a directory in your library dir called 00LOCK and does a preliminary install there. You can see that from your install of isoband:

installing to C:/Users/Léa Michel/Documents/R/win-library/4.0/00LOCK-isoband/00new/isoband/libs/x64

And at the very end of your output you can see that there is already a 00LOCK-zlibbioc directory, which means that a previous install probably had problems and only got half installed. So you need to either do

unlink("C:\Users\Léa Michel\Documents\R\win-library\4.0\00LOCK\", recursive = TRUE, force = TRUE)

Which should remove that dir, and then you can try installing zlibbioc again. You might also try

remove.packages("zlibbioc")

as well, to ensure it's fully removed.

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Entering edit mode

Ugh. You need to convert the back slashes in the call to unlink to forward slashes or R will get all huffy with you.

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Entering edit mode

I tried both (with the slashes the other way around), it did not work but I delete the package directly on my file browser and it correctly downloads the zlibbioc package. Unfortunately, I tried installing the package rtracklayer again after and it did not change anything.

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Entering edit mode

Will you give the full output that you get when installing?

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Entering edit mode

Yes, it is quite long so I had to divide it.

BiocManager::install("rtracklayer")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'rtracklayer'

  There is a binary version available but the source version is later:
            binary source needs_compilation
rtracklayer 1.49.5 1.50.0              TRUE

installing the source package ‘rtracklayer’

essai de l'URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/rtracklayer_1.50.0.tar.gz'
Content type 'application/x-gzip' length 6369416 bytes (6.1 MB)
downloaded 6.1 MB

* installing *source* package 'rtracklayer' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs

*** arch - i386
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_rtracklayer.c -o R_init_rtracklayer.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readGFF.c -o readGFF.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bbiHelper.c -o bbiHelper.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigWig.c -o bigWig.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigBedHelper.c -o bigBedHelper.o
bigBedHelper.c: In function 'bbNamedFileChunkKey':
bigBedHelper.c:148:3: warning: 'strncpy' destination unchanged after copying no bytes [-Wstringop-truncation]
   strncpy(keyBuf,item->name, maxBedNameSize);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigBed.c -o bigBed.o
bigBed.c: In function 'BBDFile_write':
bigBed.c:338:10: warning: variable 'extraIndexListEndOffset' set but not used [-Wunused-but-set-variable]
   bits64 extraIndexListEndOffset = 0;
          ^~~~~~~~~~~~~~~~~~~~~~~
bigBed.c: In function 'BBDFile_query':
bigBed.c:226:22: warning: 'typeId' may be used uninitialized in this function [-Wmaybe-uninitialized]
         switch(typeId[efIndex]) {
                      ^
bigBed.c:236:13: warning: 'lengthIndex' may be used uninitialized in this function [-Wmaybe-uninitialized]
             INTEGER(lengthIndex)[efIndex] = index + 1;
             ^~~~~~~~~~~~~~~~~~~~
bigBed.c:270:5: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized]
     SET_VECTOR_ELT(ans, index++, blocks);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:267:5: warning: 'itemRgb' may be used uninitialized in this function [-Wmaybe-uninitialized]
     SET_VECTOR_ELT(ans, index++, itemRgb);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:263:5: warning: 'thickWidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
     SET_VECTOR_ELT(ans, index++, new_IRanges("IRanges", thickStart,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                              thickWidth, R_NilValue));
                                              ~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:263:5: warning: 'thickStart' may be used uninitialized in this function [-Wmaybe-uninitialized]
bigBed.c:260:5: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized]
     SET_VECTOR_ELT(ans, index++, score);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:257:5: warning: 'name' may be used uninitialized in this function [-Wmaybe-uninitialized]
     SET_VECTOR_ELT(ans, index++, name);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chain_io.c -o chain_io.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c twoBit.c -o twoBit.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c handlers.c -o handlers.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memgfx.c -o ucsc/memgfx.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/aliType.c -o ucsc/aliType.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/binRange.c -o ucsc/binRange.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/htmlColor.c -o ucsc/htmlColor.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlList.c -o ucsc/sqlList.o
ucsc/sqlList.c: In function 'sqlLongLongArrayToString':
ucsc/sqlList.c:1041:31: warning: unknown conversion type character 'l' in format [-Wformat=]
     dyStringPrintf(string, "%lld,", array[i]);
                               ^
ucsc/sqlList.c:1041:28: warning: too many arguments for format [-Wformat-extra-args]
     dyStringPrintf(string, "%lld,", array[i]);
                            ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/tokenizer.c -o ucsc/tokenizer.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/asParse.c -o ucsc/asParse.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/basicBed.c -o ucsc/basicBed.o
ucsc/basicBed.c: In function 'lmCloneBed':
ucsc/basicBed.c:769:44: warning: argument to 'sizeof' in 'strncpy' call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess]
 strncpy(newBed->strand, bed->strand, sizeof(bed->strand));
                                            ^
ucsc/basicBed.c: In function 'cloneBed':
ucsc/basicBed.c:805:44: warning: argument to 'sizeof' in 'strncpy' call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess]
 strncpy(newBed->strand, bed->strand, sizeof(bed->strand));
                                            ^
ucsc/basicBed.c: In function 'loadAndValidateBedExt':
ucsc/basicBed.c:1619:46: warning: unknown conversion type character 'l' in format [-Wformat=]
       lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name);
                                              ^
ucsc/basicBed.c:1619:62: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
       lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name);
                                                             ~^                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                             %I64d
ucsc/basicBed.c:1619:25: warning: too many arguments for format [-Wformat-extra-args]
       lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name);
                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/basicBed.c: In function 'bedParseRgb':
ucsc/basicBed.c:997:1: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
 strncpy(dupe, itemRgb, sizeof(dupe));
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bigBed.c -o ucsc/bigBed.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:307:28: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Item index %lld greater than item count %lld in %s",
                            ^
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Entering edit mode
ucsc/bPlusTree.c:307:57: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Item index %lld greater than item count %lld in %s",
                                                         ^
ucsc/bPlusTree.c:307:64: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("Item index %lld greater than item count %lld in %s",
                                                               ~^
                                                               %I64d
  itemPos, bpt->itemCount, bpt->fileName);
  ~~~~~~~                                                        
ucsc/bPlusTree.c:307:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Item index %lld greater than item count %lld in %s",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
 bzero(summary, summarySize * sizeof(summary[0]));
 ^~~~~
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero'
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/bwgQuery.c:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
  char *blockPt, *blockEnd;
                  ^~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:238:50: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
                                                  ^
ucsc/cirTree.c:238:12: warning: too many arguments for format [-Wformat-extra-args]
 verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:45: warning: unknown conversion type character 'l' in format [-Wformat=]
     verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
                                             ^
ucsc/cirTree.c:319:16: warning: too many arguments for format [-Wformat-extra-args]
     verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c:334:54: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                      ^
ucsc/cirTree.c:334:62: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                              ^
ucsc/cirTree.c:334:72: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                                       ~^           ~~~~~~~~~~~~~~~~
                                                                       %I64d
ucsc/cirTree.c:334:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                                                                             ~^                       ~~~~~~~~~~~~~~~~~
                                                                             %I64d
ucsc/cirTree.c:334:18: warning: too many arguments for format [-Wformat-extra-args]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:38: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u.  childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
                                      ^
ucsc/cirTree.c:505:42: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
 verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u.  childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
                                         ~^                                      ~~~~~~~~~~~~~~~
                                         %I64u
ucsc/cirTree.c:505:12: warning: too many arguments for format [-Wformat-extra-args]
 verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u.  childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:32: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
                                ^
ucsc/cirTree.c:585:47: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
 verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
                                              ~^                ~~~~~~~~~~~~~~~
                                              %I64d
ucsc/cirTree.c:585:12: warning: too many arguments for format [-Wformat-extra-args]
 verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2476:31: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
                               ^
ucsc/common.c:2476:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
                                         ~^     ~~~~~~~~~~~~~~~
                                         %I64d
ucsc/common.c:2476:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:28: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
                            ^
ucsc/common.c:2487:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
                                      ~^   ~~~~~~~~~~~~~~~
                                      %I64d
ucsc/common.c:2487:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2489:34: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %lld bytes", (long long)size);
                                  ^
ucsc/common.c:2489:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("End of file reading %lld bytes", (long long)size);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:30: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("Error reading %lld bytes", (long long)size);
                              ^
ucsc/common.c:2630:13: warning: too many arguments for format [-Wformat-extra-args]
  errnoAbort("Error reading %lld bytes", (long long)size);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2632:34: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
                                  ^
ucsc/common.c:2632:50: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
                                                  ^
ucsc/common.c:2632:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2647:44: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
                                            ^
ucsc/common.c:2647:52: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
                                                    ^
ucsc/common.c:2647:18: warning: too many arguments for format [-Wformat-extra-args]
         errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2658:29: warning: unknown conversion type character 'l' in format [-Wformat=]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                             ^
ucsc/common.c:2658:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                                 ~^                    ~~~~~~~~~~~~~~~~~
                                 %I64d
ucsc/common.c:2658:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                                     ~^
                                     %s
         ((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2658:16: warning: too many arguments for format [-Wformat-extra-args]
     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:60: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
                                                            ^
ucsc/common.c:2785:65: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
                                                                 ^
ucsc/common.c:2785:18: warning: too many arguments for format [-Wformat-extra-args]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:39: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
                                       ^
ucsc/common.c:3251:58: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
                                                          ^
ucsc/common.c:3251:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:39: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
                                       ^
ADD REPLY
0
Entering edit mode
ucsc/common.c:3260:61: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
                                                             ^
ucsc/common.c:3260:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:39: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
                                       ^
ucsc/common.c:3276:62: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
                                                              ^
ucsc/common.c:3276:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:39: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
                                       ^
ucsc/common.c:3285:62: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
                                                              ^
ucsc/common.c:3285:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnaseq.c -o ucsc/dnaseq.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnautil.c -o ucsc/dnautil.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:34: warning: unknown conversion type character 'l' in format [-Wformat=]
 safef(pidStr, sizeof(pidStr), "%lld",  ptrToLL(pid));
                                  ^
ucsc/errAbort.c:356:31: warning: too many arguments for format [-Wformat-extra-args]
 safef(pidStr, sizeof(pidStr), "%lld",  ptrToLL(pid));
                               ^~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hash.c -o ucsc/hash.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:56: warning: unknown conversion type character 'l' in format [-Wformat=]
  safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
                                                        ^
ucsc/linefile.c:1083:28: warning: too many arguments for format [-Wformat-extra-args]
  safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
 static char * headerBytes(char *fileName, int numbytes)
               ^~~~~~~~~~~
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
 static char **getDecompressor(char *fileName)
               ^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:35: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
                                   ^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlNum.c -o ucsc/sqlNum.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:51:36: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Couldn't zCompress %lld bytes: %s",
                                    ^
ucsc/zlibFace.c:51:47: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
     errAbort("Couldn't zCompress %lld bytes: %s",
                                              ~^
                                              %I64d
      (long long)uncompressedSize, zlibErrorMessage(err));
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~               
ucsc/zlibFace.c:51:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Couldn't zCompress %lld bytes: %s",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:72:38: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Couldn't zUncompress %lld bytes: %s",
                                      ^
ucsc/zlibFace.c:72:49: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
     errAbort("Couldn't zUncompress %lld bytes: %s",
                                                ~^
                                                %I64d
      (long long)compressedSize, zlibErrorMessage(err));
      ~~~~~~~~~~~~~~~~~~~~~~~~~                   
ucsc/zlibFace.c:72:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Couldn't zUncompress %lld bytes: %s",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dystring.c -o ucsc/dystring.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hmmstats.c -o ucsc/hmmstats.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                   ^
ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                          ^
ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                                 ^
ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                                        ^
ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                                               ^
ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
ADD REPLY
0
Entering edit mode
                   ^
ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                          ^
ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                                 ^
ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                                        ^
ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                                               ^
ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                   ^
ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                          ^
ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                 ^
ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                        ^
ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                   ^
ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                          ^
ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                 ^
ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                                        ^
ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                   ^
ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                          ^
ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                                 ^
ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                   ^
ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                          ^
ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                                 ^
ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
                ^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                   ^
ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                          ^
ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld", thousands, l);
                ^~~~~~~~~~~~~
ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                   ^
ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
                          ^
ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld,%03lld", thousands, l);
                ^~~~~~~~~~~~~
ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
                   ^
ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld", l);
                ^~~~~~
ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
                   ^
ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args]
     sprintf(s, "%lld", l);
                ^~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/pipeline.c -o ucsc/pipeline.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rangeTree.c -o ucsc/rangeTree.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rbTree.c -o ucsc/rbTree.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:90:50: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
                                                  ^
ucsc/memalloc.c:90:69: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
                                                                     ^
ucsc/memalloc.c:90:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:93:60: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                            ^
ucsc/memalloc.c:93:78: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                                             ~^
                                                                             %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                         
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:113:56: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
                                                        ^
ucsc/memalloc.c:113:75: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
                                                                           ^
ucsc/memalloc.c:113:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:116:66: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
                                                                  ^
ucsc/memalloc.c:116:84: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
                                                                                   ~^
                                                                                   %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                               
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:138:64: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
                                                                ^
ucsc/memalloc.c:138:82: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
                                                                                 ~^
                                                                                 %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                             
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:160:67: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
                                                                   ^
ucsc/memalloc.c:160:85: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
                                                                                    ~^
                                                                                    %I64d
  (unsigned long long)size, errno);
  ~~~~~~~~~~~~~~~~~~~~~~~~                                                            
ucsc/memalloc.c:160:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:186:45: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
                                             ^
ucsc/memalloc.c:186:64: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
                                                                ^
ucsc/memalloc.c:186:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:189:55: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                       ^
ucsc/memalloc.c:189:73: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
                                                                        ~^
                                                                        %I64d
              (unsigned long long)size, errno);
              ~~~~~~~~~~~~~~~~~~~~~~~~                                    
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:325:45: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
                                             ^
ucsc/memalloc.c:325:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:331:49: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
                                                 ^
ucsc/memalloc.c:331:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:376:70: warning: unknown conversion type character 'l' in format [-Wformat=]
         safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie,
                                                                      ^
ucsc/memalloc.c:376:38: warning: too many arguments for format [-Wformat-extra-args]
         safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie,
                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:383:74: warning: unknown conversion type character 'l' in format [-Wformat=]
         safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
                                                                          ^
ucsc/memalloc.c:383:38: warning: too many arguments for format [-Wformat-extra-args]
         safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dlist.c -o ucsc/dlist.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:138:58: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
                                                          ^
ucsc/udc.c:138:13: warning: too many arguments for format [-Wformat-extra-args]
  errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:143:43: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
                                           ^
ucsc/udc.c:143:62: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
                                                              ^
ucsc/udc.c:143:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
ADD REPLY
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Entering edit mode
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:234:49: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
                                                 ^
ucsc/udc.c:234:58: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
 verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
                                                         ~^           ~~~~~~
                                                         %I64d
ucsc/udc.c:234:12: warning: too many arguments for format [-Wformat-extra-args]
 verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:241:57: warning: unknown conversion type character 'l' in format [-Wformat=]
     warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
                                                         ^
ucsc/udc.c:241:10: warning: too many arguments for format [-Wformat-extra-args]
     warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:290:54: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
                                                      ^
ucsc/udc.c:290:63: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
 verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
                                                              ~^           ~~~~~~
                                                              %I64d
ucsc/udc.c:290:12: warning: too many arguments for format [-Wformat-extra-args]
 verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:308:53: warning: unknown conversion type character 'l' in format [-Wformat=]
  warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
                                                     ^
ucsc/udc.c:308:7: warning: too many arguments for format [-Wformat-extra-args]
  warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:515:42: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
                                          ^
ucsc/udc.c:515:80: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
     errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
                                                                               ~^
                                                                               %I64d
       fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
                                 ~~~~~~                                          
ucsc/udc.c:515:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:665:40: warning: unknown conversion type character 'l' in format [-Wformat=]
  verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
                                        ^
ucsc/udc.c:665:48: warning: unknown conversion type character 'l' in format [-Wformat=]
  verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
                                                ^
ucsc/udc.c:665:56: warning: unknown conversion type character 'l' in format [-Wformat=]
  verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
                                                        ^
ucsc/udc.c:665:64: warning: unknown conversion type character 'l' in format [-Wformat=]
  verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
                                                                ^
ucsc/udc.c:665:71: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
  verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
                                                                      ~^
                                                                      %I64d
ucsc/udc.c:667:3:
   bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
   ~~~~~~~~~~~~~~~~~~                                                   
ucsc/udc.c:665:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
  verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:667:23:
   bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:666:17: note: format string is defined here
   "new version %d\n",
                ~^
                %I64d
ucsc/udc.c:665:13: warning: too many arguments for format [-Wformat-extra-args]
  verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1110:52: warning: unknown conversion type character 'l' in format [-Wformat=]
     warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
                                                    ^
ucsc/udc.c:1110:58: warning: unknown conversion type character 'l' in format [-Wformat=]
     warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
                                                          ^
ucsc/udc.c:1110:10: warning: too many arguments for format [-Wformat-extra-args]
     warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1135:30: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
                              ^
ucsc/udc.c:1135:45: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
                                            ~^
                                            %I64d
    readSize, file->url, startPos, actualSize);
    ~~~~~~~~                                  
ucsc/udc.c:1135:50: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
                                                  ^
ucsc/udc.c:1135:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
                                                          ~^
                                                          %s
    readSize, file->url, startPos, actualSize);
              ~~~~~~~~~                                     
ucsc/udc.c:1135:11: warning: too many arguments for format [-Wformat-extra-args]
  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1361:35: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
                                   ^
ucsc/udc.c:1361:50: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
                                                 ~^                  ~~~~
                                                 %I64d
ucsc/udc.c:1361:64: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
                                                                ^
ucsc/udc.c:1361:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1496:23: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
                       ^
ucsc/udc.c:1496:68: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
                                                                    ^
ucsc/udc.c:1496:14: warning: too many arguments for format [-Wformat-extra-args]
     errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
ucsc/udc.c:126:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
 static void readAndIgnore(int sd, bits64 size)
             ^~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/net.c -o ucsc/net.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bits.c -o ucsc/bits.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/twoBit.c -o ucsc/twoBit.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/internet.c -o ucsc/internet.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/https.c -o ucsc/https.o
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Entering edit mode
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/base64.c -o ucsc/base64.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/verbose.c -o ucsc/verbose.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/os.c -o ucsc/os.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/wildcmp.c -o ucsc/wildcmp.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/include" -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG  -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/S4Vectors/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/IRanges/include' -I'C:/Users/Léa Michel/Documents/R/win-library/4.0/XVector/include'        -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/aliType.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -LC:/Users/Léa Michel/Documents/R/win-library/4.0/zlibbioc/libs/i386 -lzlib1bioc -lws2_32 -LC:/PROGRA~1/R/R-40~1.2/bin/i386 -lR
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lzlib1bioc
collect2.exe: error: ld returned 1 exit status
aucune DLL n'a pas été créé
ERROR: compilation failed for package 'rtracklayer'
* removing 'C:/Users/Léa Michel/Documents/R/win-library/4.0/rtracklayer'

The downloaded source packages are in
    ‘C:\Users\Léa Michel\AppData\Local\Temp\Rtmp6rMZIy\downloaded_packages’
Old packages: 'ipred', 'tinytex'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
        binary source needs_compilation
ipred    0.9-9 0.9-10              TRUE
tinytex   0.29   0.30             FALSE

installing the source packages ‘ipred’, ‘tinytex’

essai de l'URL 'https://cran.rstudio.com/src/contrib/ipred_0.9-10.tar.gz'
Content type 'application/x-gzip' length 178797 bytes (174 KB)
downloaded 174 KB

essai de l'URL 'https://cran.rstudio.com/src/contrib/tinytex_0.30.tar.gz'
Content type 'application/x-gzip' length 28839 bytes (28 KB)
downloaded 28 KB

* installing *source* package 'ipred' ...
** package 'ipred' correctement décompressé et sommes MD5 vérifiées
** using staged installation
** libs

*** arch - i386
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG          -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SdiffKM.c -o SdiffKM.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG          -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o ipred.dll tmp.def SdiffKM.o init.o -LC:/PROGRA~1/R/R-40~1.2/bin/i386 -lR
installing to C:/Users/Léa Michel/Documents/R/win-library/4.0/00LOCK-ipred/00new/ipred/libs/i386

*** arch - x64
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG          -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SdiffKM.c -o SdiffKM.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG          -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o ipred.dll tmp.def SdiffKM.o init.o -LC:/PROGRA~1/R/R-40~1.2/bin/x64 -lR
installing to C:/Users/Léa Michel/Documents/R/win-library/4.0/00LOCK-ipred/00new/ipred/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ipred'
    finding HTML links ... fini
    DLBCL                                   html  
    GlaucomaMVF                             html  
    Smoking                                 html  
    bagging                                 html  
    bootest                                 html  
    control.errorest                        html  
    cv                                      html  
    dystrophy                               html  
    errorest                                html  
    inbagg                                  html  
    inclass                                 html  
    ipred-internal                          html  
    ipredknn                                html  
    kfoldcv                                 html  
    mypredict.lm                            html  
    predict.bagging                         html  
    predict.inbagg                          html  
    predict.inclass                         html  
    predict.ipredknn                        html  
    predict.slda                            html  
    print.bagging                           html  
    print.cvclass                           html  
    print.inbagg                            html  
    print.inclass                           html  
    prune.bagging                           html  
    rsurv                                   html  
    sbrier                                  html  
    slda                                    html  
    summary.bagging                         html  
    summary.inbagg                          html  
    summary.inclass                         html  
    varset                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (ipred)
* installing *source* package 'tinytex' ...
** package 'tinytex' correctement décompressé et sommes MD5 vérifiées
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'tinytex'
    finding HTML links ... fini
    check_installed                         html  
    copy_tinytex                            html  
    install_tinytex                         html  
    is_tinytex                              html  
    latexmk                                 html  
    parse_install                           html  
    parse_packages                          html  
    r_texmf                                 html  
    tl_pkgs                                 html  
    tl_sizes                                html  
    tlmgr                                   html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (tinytex)

The downloaded source packages are in
    ‘C:\Users\Léa Michel\AppData\Local\Temp\Rtmp6rMZIy\downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘rtracklayer’ had non-zero exit status
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Entering edit mode

OK. That's super weird. What do you get from

> dir(system.file("libs/i386", package = "zlibbioc"))
[1] "libzbioc.a"    "zlib1bioc.dll" "zlibbioc.dll"
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Entering edit mode

I get the same thing as you

dir(system.file("libs/i386", package = "zlibbioc"))
[1] "libzbioc.a"    "zlib1bioc.dll" "zlibbioc.dll"

I put the output that I got when installing rtracklayer, not zlibbiocif if that was what you were asking.

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Entering edit mode
@james-w-macdonald-5106
Last seen 16 hours ago
United States

I'm adding another answer because the comments are getting so janky.

At the end it does this:

C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/aliType.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -LC:/Users/jmacdon/AppData/Roaming/R/win-library/4.0/zlibbioc/libs/i386 -lzlib1bioc -lws2_32 -Lc:/PROGRA~1/R/R-40~1.0/bin/i386 -lR

The one difference is that there are no spaces or ecrit marks in my path to my libbioc. You could try using .libPaths to create a different library dir, and then install zlibbioc and try re-installing rtracklayer. Or just accept the binary install. If you have any more questions, please do a new post. This one is too long now.

0
Entering edit mode

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