Cannot install oligo on Fedora
0
0
Entering edit mode
Guido Hooiveld ★ 4.1k
@guido-hooiveld-2020
Last seen 2 days ago
Wageningen University, Wageningen, the …

I upgraded my R and Bioconductor installation on my Fedora machine. Upgrading all packages went fine, except for oligo.

The reported errors are rather cryptic to me, so I would appreciate some pointers to fix this.

> BiocManager::install(c('oligo'),force=TRUE)
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 (2024-04-24)
Installing package(s) 'oligo'
trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/oligo_1.68.0.tar.gz'
Content type 'application/x-gzip' length 28421969 bytes (27.1 MB)
==================================================
downloaded 27.1 MB

* installing *source* package 'oligo' ...
** using staged installation
** libs
using C compiler: 'gcc (GCC) 14.1.1 20240507 (Red Hat 14.1.1-1)'
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib64/R/library/preprocessCore/include' -I/usr/local/include    -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -c DABG.c -o DABG.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib64/R/library/preprocessCore/include' -I/usr/local/include    -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c: In function 'gzcountLines':
ParserGzXYS.c:18:17: error: passing argument 1 of 'gzeof' from incompatible pointer type [-Wincompatible-pointer-types]
   18 |   while (!gzeof(file)){
      |                 ^~~~
      |                 |
      |                 struct gzFile_s **
In file included from ParserGzXYS.c:4:
/usr/include/zlib.h:1575:36: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **'
 1575 | Z_EXTERN int Z_EXPORT gzeof(gzFile file);
      |                             ~~~~~~~^~~~
ParserGzXYS.c:19:12: error: passing argument 1 of 'gzgets' from incompatible pointer type [-Wincompatible-pointer-types]
   19 |     gzgets(file, buffer, 1000);
      |            ^~~~
      |            |
      |            struct gzFile_s **
/usr/include/zlib.h:1472:40: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **'
 1472 | Z_EXTERN char * Z_EXPORT gzgets(gzFile file, char *buf, int len);
      |                                 ~~~~~~~^~~~
ParserGzXYS.c: In function 'gzxys_header_field':
ParserGzXYS.c:46:6: error: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types]
   46 |   fp = gzopen(currentFile, "rb");
      |      ^
ParserGzXYS.c:50:10: error: passing argument 1 of 'gzgets' from incompatible pointer type [-Wincompatible-pointer-types]
   50 |   gzgets(fp, buffer, LINEMAX);
      |          ^~
      |          |
      |          struct gzFile_s **
/usr/include/zlib.h:1472:40: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **'
 1472 | Z_EXTERN char * Z_EXPORT gzgets(gzFile file, char *buf, int len);
      |                                 ~~~~~~~^~~~
ParserGzXYS.c:51:11: error: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
   51 |   gzclose(fp);
      |           ^~
      |           |
      |           struct gzFile_s **
/usr/include/zlib.h:1611:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **'
 1611 | Z_EXTERN int Z_EXPORT gzclose(gzFile file);
      |                               ~~~~~~~^~~~
ParserGzXYS.c: In function 'R_read_gzxys_files':
ParserGzXYS.c:134:6: error: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types]
  134 |   fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb");
      |      ^
ParserGzXYS.c:138:11: error: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
  138 |   gzclose(fp);
      |           ^~
      |           |
      |           struct gzFile_s **
/usr/include/zlib.h:1611:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **'
 1611 | Z_EXTERN int Z_EXPORT gzclose(gzFile file);
      |                               ~~~~~~~^~~~
make: *** [/usr/lib64/R/etc/Makeconf:195: ParserGzXYS.o] Error 1
ERROR: compilation failed for package 'oligo'
* removing '/usr/lib64/R/library/oligo'
* restoring previous '/usr/lib64/R/library/oligo'

The downloaded source packages are in
        '/tmp/Rtmpv8fwJD/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Old packages: 'oligo'
Update all/some/none? [a/s/n]: n
 Warning message:
In install.packages(...) :
  installation of package 'oligo' had non-zero exit status
> 


> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-redhat-linux-gnu
Running under: Fedora Linux 40 (Forty)

Matrix products: default
BLAS/LAPACK: FlexiBLAS OPENBLAS-OPENMP;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Amsterdam
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
[1] compiler_4.4.0
>
oligo source Install • 1.0k views
ADD COMMENT •
0
Entering edit mode

What version of zlib are you running? I can compile with 1.2.7

ADD REPLY •
0
Entering edit mode

Aha, that is a good one!

Starting from release 40, as I just found out, Fedora apparently is not including/using zlib as such anymore, but has changed to zlib-ng. See e.g. here or here.

Compatibility would be maintained through zlib-ng-compat, which would provide zlib 1.2.13.

Currently installed on my machine: zlib-ng-compat-2.1.6-2.fc40. Link.

So it seems oligo is not compatible with zlib 1.2.13?

ADD REPLY •
0
Entering edit mode

There is the zlibbioc package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would require intervention on your part to redirect the makefile to use zlibbioc instead of the system headers.

ADD REPLY •
0
Entering edit mode

Wait a minute. The oligo package is supposed to be using zlibbioc, but apparently it is not. I get the same thing as you do, where it's pointing to the system zlib header instead of zlib.h in the zlibbioc package.

ADD REPLY •
0
Entering edit mode

so whats the solution for this error?

ADD REPLY •
0
Entering edit mode

I think the solution is for the C code in oligo to be updated to work with more modern versions of zlib. The zlibbioc package is really meant to allow Windows users to use zlib, rather than as a header source for *nix based computers (the version of zlib is quite old, and a bunch of the underlying functions are remapped to have bioc_ prepended), so using zlibbioc is just a kludge that is likely suboptimal. It might just be easier to fix the C code instead.

ADD REPLY •
0
Entering edit mode

Thanks for all suggestions and getting to the bottom of this! Unfortunately, fixing C code goes way above my skill level, so I cannot contribute to that.

ADD REPLY •
1
Entering edit mode

FYI, I emailed Benilton and he says he's working on a fix, so stay tuned!

ADD REPLY •
0
Entering edit mode

Thanks James for your continuous attention to this!

Meanwhile Benilton has fixed the zlib problem (thanks for that as well!), and oligo installed fine now.

> packageVersion('oligo')
[1] '1.68.2'
>

For completeness:

> library(oligo)
> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-redhat-linux-gnu
Running under: Fedora Linux 40 (Forty)

Matrix products: default
BLAS/LAPACK: FlexiBLAS OPENBLAS-OPENMP;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Amsterdam
tzcode source: system (glibc)

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

other attached packages:
[1] oligo_1.68.2        Biostrings_2.72.1   GenomeInfoDb_1.40.1
[4] XVector_0.44.0      IRanges_2.38.0      S4Vectors_0.42.0   
[7] Biobase_2.64.0      oligoClasses_1.66.0 BiocGenerics_0.50.0

loaded via a namespace (and not attached):
 [1] Matrix_1.7-0                bit_4.0.5                  
 [3] preprocessCore_1.66.0       jsonlite_1.8.8             
 [5] compiler_4.4.0              BiocManager_1.30.23        
 [7] crayon_1.5.2                SummarizedExperiment_1.34.0
 [9] blob_1.2.4                  affxparser_1.76.0          
[11] GenomicRanges_1.56.0        splines_4.4.0              
[13] fastmap_1.2.0               lattice_0.22-6             
[15] R6_2.5.1                    S4Arrays_1.4.1             
[17] ff_4.0.12                   iterators_1.0.14           
[19] DelayedArray_0.30.1         MatrixGenerics_1.16.0      
[21] GenomeInfoDbData_1.2.12     DBI_1.2.3                  
[23] rlang_1.1.4                 affyio_1.74.0              
[25] cachem_1.1.0                bit64_4.0.5                
[27] memoise_2.0.1               cli_3.6.2                  
[29] RSQLite_2.3.7               SparseArray_1.4.8          
[31] zlibbioc_1.50.0             foreach_1.5.2              
[33] grid_4.4.0                  vctrs_0.6.5                
[35] codetools_0.2-20            abind_1.4-5                
[37] httr_1.4.7                  matrixStats_1.3.0          
[39] tools_4.4.0                 UCSC.utils_1.0.0           
>
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 950 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6