Error downloading Homo.sapiens package
0
2
Entering edit mode
@noemicarrascoyepes-24320
Last seen 4.2 years ago

Hi, I can't seem to download the Homo.sapiens or the BSgenome.Hsapiens.UCSC.hg19 package. These are my errors:

For the Homo.sapiens package:

> BiocManager::install("Homo.sapiens")
Bioconductor version 3.11 (BiocManager 1.30.10), R
  4.0.2 (2020-06-22)
Installing package(s) 'Homo.sapiens'
also installing the dependencies ‘GO.db’, ‘org.Hs.eg.db’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

installing the source packages ‘GO.db’, ‘org.Hs.eg.db’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘Homo.sapiens’

trying URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GO.db_3.11.4.tar.gz'
Content type 'application/x-gzip' length 31975305 bytes (30.5 MB)
downloaded 30.5 MB

trying URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/org.Hs.eg.db_3.11.4.tar.gz'
Content type 'application/x-gzip' length 79959831 bytes (76.3 MB)
downloaded 76.3 MB

trying URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz'
Content type 'application/x-gzip' length 18669702 bytes (17.8 MB)
downloaded 17.8 MB

trying URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/Homo.sapiens_1.3.1.tar.gz'
Content type 'application/x-gzip' length 1617 bytes
downloaded 1617 bytes

* installing *source* package 'GO.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GO.db'
    finding HTML links ... done
    GOBASE                                  html  
    GOBPANCESTOR                            html  
    GOBPCHILDREN                            html  
    GOBPOFFSPRING                           html  
    GOBPPARENTS                             html  
    GOCCANCESTOR                            html  
    GOCCCHILDREN                            html  
    GOCCOFFSPRING                           html  
    GOCCPARENTS                             html  
    GOMAPCOUNTS                             html  
    GOMFANCESTOR                            html  
    GOMFCHILDREN                            html  
    GOMFOFFSPRING                           html  
    GOMFPARENTS                             html  
    GOOBSOLETE                              html  
    GOSYNONYM                               html  
    GOTERM                                  html  
    GO_dbconn                               html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
Error: package or namespace load failed for 'GO.db':
 .onLoad failed in loadNamespace() for 'GO.db', details:
  call: NULL
  error: Failed to load extension: The specified module could not be found.

Error: loading failed
Execution halted
*** arch - x64
Error: package or namespace load failed for 'GO.db':
 .onLoad failed in loadNamespace() for 'GO.db', details:
  call: NULL
  error: Failed to load extension: The specified module could not be found.

Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing 'C:/Users/Noemí/Documents/R/win-library/4.0/GO.db'
* installing *source* package 'org.Hs.eg.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'org.Hs.eg.db'
    finding HTML links ... done
    org.Hs.egACCNUM                         html  
    org.Hs.egALIAS2EG                       html  
    org.Hs.egBASE                           html  
    org.Hs.egCHR                            html  
    org.Hs.egCHRLENGTHS                     html  
    org.Hs.egCHRLOC                         html  
    org.Hs.egENSEMBL                        html  
    org.Hs.egENSEMBLPROT                    html  
    org.Hs.egENSEMBLTRANS                   html  
    org.Hs.egENZYME                         html  
    org.Hs.egGENENAME                       html  
    org.Hs.egGO                             html  
    org.Hs.egMAP                            html  
    org.Hs.egMAPCOUNTS                      html  
    org.Hs.egOMIM                           html  
    org.Hs.egORGANISM                       html  
    org.Hs.egPATH                           html  
    org.Hs.egPFAM                           html  
    org.Hs.egPMID                           html  
    org.Hs.egPROSITE                        html  
    org.Hs.egREFSEQ                         html  
    org.Hs.egSYMBOL                         html  
    org.Hs.egUCSCKG                         html  
    org.Hs.egUNIGENE                        html  
    org.Hs.egUNIPROT                        html  
    org.Hs.eg_dbconn                        html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
Error: package or namespace load failed for 'org.Hs.eg.db':
 .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
  call: NULL
  error: Failed to load extension: The specified module could not be found.

Error: loading failed
Execution halted
*** arch - x64
Error: package or namespace load failed for 'org.Hs.eg.db':
 .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
  call: NULL
  error: Failed to load extension: The specified module could not be found.

Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing 'C:/Users/Noemí/Documents/R/win-library/4.0/org.Hs.eg.db'
* installing *source* package 'TxDb.Hsapiens.UCSC.hg19.knownGene' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TxDb.Hsapiens.UCSC.hg19.knownGene'
    finding HTML links ... done
    package                                 html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
Error: package or namespace load failed for 'TxDb.Hsapiens.UCSC.hg19.knownGene':
 .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
  call: NULL
  error: Failed to load extension: The specified module could not be found.

Error: loading failed
Execution halted
*** arch - x64
Error: package or namespace load failed for 'TxDb.Hsapiens.UCSC.hg19.knownGene':
 .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
  call: NULL
  error: Failed to load extension: The specified module could not be found.

Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing 'C:/Users/Noemí/Documents/R/win-library/4.0/TxDb.Hsapiens.UCSC.hg19.knownGene'
ERROR: dependencies 'GO.db', 'org.Hs.eg.db', 'TxDb.Hsapiens.UCSC.hg19.knownGene' are not available for package 'Homo.sapiens'
* removing 'C:/Users/Noemí/Documents/R/win-library/4.0/Homo.sapiens'

The downloaded source packages are in
    ‘C:\Users\Noemí\AppData\Local\Temp\Rtmpcx7qMW\downloaded_packages’
Installation path not writeable, unable to update
  packages: MASS, mgcv, nlme, survival
Old packages: 'callr', 'clipr', 'ps', 'rlang'
Update all/some/none? [a/s/n]: 
n
Warning messages:
1: In install.packages(...) :
  installation of package ‘GO.db’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘Homo.sapiens’ had non-zero exit status

For the BSgenome.Hsapiens.UCSC.hg19:

> BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
Bioconductor version 3.11 (BiocManager 1.30.10), R
  4.0.2 (2020-06-22)
Installing package(s) 'BSgenome.Hsapiens.UCSC.hg19'
installing the source package ‘BSgenome.Hsapiens.UCSC.hg19’

trying URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz'
Content type 'application/x-gzip' length 710245413 bytes (677.3 MB)
downloaded 677.3 MB

* installing *source* package 'BSgenome.Hsapiens.UCSC.hg19' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BSgenome.Hsapiens.UCSC.hg19'
    finding HTML links ... done
    package                                 html  
Rd warning: C:/Users/Noemí/AppData/Local/Temp/RtmpYLyBEs/R.INSTALL88d01bfa24d0/BSgenome.Hsapiens.UCSC.hg19/man/package.Rd:33: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/Noemí/AppData/Local/Temp/RtmpYLyBEs/R.INSTALL88d01bfa24d0/BSgenome.Hsapiens.UCSC.hg19/man/package.Rd:36: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
Warning in .seqlengths_TwoBitFile(x) :
  mustOpen: Can't open C:/Users/Noemí/Documents/R/win-library/4.0/00LOCK-BSgenome.Hsapiens.UCSC.hg19/00new/BSgenome.Hsapiens.UCSC.hg19/extdata/single_sequences.2bit to read: No such file or directory
Error: package or namespace load failed for 'BSgenome.Hsapiens.UCSC.hg19':
 .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:
  call: h(simpleError(msg, call))
  error: error in evaluating the argument 'x' in selecting a method for function 'seqlengths': UCSC library operation failed
Error: loading failed
Execution halted
*** arch - x64
Warning in .seqlengths_TwoBitFile(x) :
  mustOpen: Can't open C:/Users/Noemí/Documents/R/win-library/4.0/00LOCK-BSgenome.Hsapiens.UCSC.hg19/00new/BSgenome.Hsapiens.UCSC.hg19/extdata/single_sequences.2bit to read: No such file or directory
Error: package or namespace load failed for 'BSgenome.Hsapiens.UCSC.hg19':
 .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:
  call: h(simpleError(msg, call))
  error: error in evaluating the argument 'x' in selecting a method for function 'seqlengths': UCSC library operation failed
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing 'C:/Users/Noemí/Documents/R/win-library/4.0/BSgenome.Hsapiens.UCSC.hg19'

The downloaded source packages are in
    ‘C:\Users\Noemí\AppData\Local\Temp\Rtmpcx7qMW\downloaded_packages’
Installation path not writeable, unable to update
  packages: MASS, mgcv, nlme, survival
Old packages: 'callr', 'clipr', 'ps', 'rlang'
Update all/some/none? [a/s/n]: 
n
Warning message:
In install.packages(...) :
  installation of package ‘BSgenome.Hsapiens.UCSC.hg19’ had non-zero exit status

This is my session info:

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=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] BSgenome_1.56.0            
 [2] gwascat_2.20.1             
 [3] GenomicAlignments_1.24.0   
 [4] Rsamtools_2.4.0            
 [5] SummarizedExperiment_1.18.2
 [6] DelayedArray_0.14.1        
 [7] matrixStats_0.57.0         
 [8] rtracklayer_1.48.0         
 [9] Biostrings_2.56.0          
[10] XVector_0.28.0             
[11] ERBS_1.0                   
[12] devtools_2.3.2             
[13] usethis_1.6.3              
[14] GenomicFeatures_1.40.1     
[15] AnnotationDbi_1.50.3       
[16] Biobase_2.48.0             
[17] GenomicRanges_1.40.0       
[18] GenomeInfoDb_1.24.2        
[19] IRanges_2.22.2             
[20] S4Vectors_0.26.1           
[21] BiocGenerics_0.34.0        

loaded via a namespace (and not attached):
 [1] bitops_1.0-6           fs_1.5.0              
 [3] bit64_4.0.5            progress_1.2.2        
 [5] httr_1.4.2             rprojroot_1.3-2       
 [7] tools_4.0.2            backports_1.1.10      
 [9] R6_2.4.1               DBI_1.1.0             
[11] colorspace_1.4-1       withr_2.3.0           
[13] tidyselect_1.1.0       prettyunits_1.1.1     
[15] processx_3.4.4         bit_4.0.4             
[17] curl_4.3               compiler_4.0.2        
[19] cli_2.0.2              desc_1.2.0            
[21] scales_1.1.1           callr_3.4.4           
[23] askpass_1.1            rappdirs_0.3.1        
[25] stringr_1.4.0          digest_0.6.25         
[27] pkgconfig_2.0.3        sessioninfo_1.1.1     
[29] dbplyr_1.4.4           rlang_0.4.7           
[31] rstudioapi_0.11        RSQLite_2.2.1         
[33] generics_0.0.2         BiocParallel_1.22.0   
[35] dplyr_1.0.2            RCurl_1.98-1.2        
[37] magrittr_1.5           GenomeInfoDbData_1.2.3
[39] Matrix_1.2-18          Rcpp_1.0.5            
[41] munsell_0.5.0          fansi_0.4.1           
[43] lifecycle_0.2.0        stringi_1.5.3         
[45] zlibbioc_1.34.0        pkgbuild_1.1.0        
[47] BiocFileCache_1.12.1   grid_4.0.2            
[49] blob_1.2.1             crayon_1.3.4          
[51] lattice_0.20-41        hms_0.5.3             
[53] ps_1.3.4               pillar_1.4.6          
[55] biomaRt_2.44.1         pkgload_1.1.0         
[57] XML_3.99-0.5           glue_1.4.2            
[59] remotes_2.2.0          BiocManager_1.30.10   
[61] vctrs_0.3.4            testthat_2.3.2        
[63] gtable_0.3.0           openssl_1.4.3         
[65] purrr_0.3.4            assertthat_0.2.1      
[67] ggplot2_3.3.2          tibble_3.0.3          
[69] memoise_1.1.0          ellipsis_0.3.1

Thank you!!!
Homosapiens • 2.6k views
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0
Entering edit mode

Could you see what ERROR's are displayed when trying to load GO.db BiocManager::install('GO.db') ? and could you see if BiocManager::valid() offers any needed updates or mismatches?

ADD REPLY •
0
Entering edit mode

I have the same problem. See code below. I cannot download any genome from BSgenome.

> BiocManager::valid()
[1] TRUE
> BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'BSgenome.Hsapiens.UCSC.hg38'
installing the source package ‘BSgenome.Hsapiens.UCSC.hg38’

trying URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.3.tar.gz'
Content type 'application/x-gzip' length 721596676 bytes (688.2 MB)
downloaded 688.2 MB

* installing *source* package 'BSgenome.Hsapiens.UCSC.hg38' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BSgenome.Hsapiens.UCSC.hg38'
    finding HTML links ... done
    package                                 html  
Rd warning: C:/Users/Philipp/AppData/Local/Temp/RtmpQzgv0b/R.INSTALL12c828876f51/BSgenome.Hsapiens.UCSC.hg38/man/package.Rd:33: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/Philipp/AppData/Local/Temp/RtmpQzgv0b/R.INSTALL12c828876f51/BSgenome.Hsapiens.UCSC.hg38/man/package.Rd:36: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
Warning in .seqlengths_TwoBitFile(x) :
  mustOpen: Can't open C:/Users/Philipp/Documents/R/win-library/4.0/00LOCK-BSgenome.Hsapiens.UCSC.hg38/00new/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory
Error: package or namespace load failed for 'BSgenome.Hsapiens.UCSC.hg38':
 .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38', details:
  call: h(simpleError(msg, call))
  error: error in evaluating the argument 'x' in selecting a method for function 'seqlengths': UCSC library operation failed
Error: loading failed
Execution halted
*** arch - x64
Warning in .seqlengths_TwoBitFile(x) :
  mustOpen: Can't open C:/Users/Philipp/Documents/R/win-library/4.0/00LOCK-BSgenome.Hsapiens.UCSC.hg38/00new/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory
Error: package or namespace load failed for 'BSgenome.Hsapiens.UCSC.hg38':
 .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38', details:
  call: h(simpleError(msg, call))
  error: error in evaluating the argument 'x' in selecting a method for function 'seqlengths': UCSC library operation failed
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing 'C:/Users/Philipp/Documents/R/win-library/4.0/BSgenome.Hsapiens.UCSC.hg38'

The downloaded source packages are in
    ‘C:\Users\Philipp\AppData\Local\Temp\RtmpcNWjev\downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘BSgenome.Hsapiens.UCSC.hg38’ had non-zero exit status
ADD REPLY •
0
Entering edit mode

Also here, does your user name have non-ASCII characters? And can you 

BiocManager::install("BSgenome.Hsapiens.UCSC.hg19", INSTALL_opts = "--no-staged-install")

?

ADD REPLY •
0
Entering edit mode

i think the problem here might be the non-ASCII character in the user name. Can you try

BiocManager::install("BSgenome.Hsapiens.UCSC.hg19", INSTALL_opts = "--no-staged-install")

? And if possible try installing as a user or into a library path (the first entry in .libPaths()) that has only ASCII characters in the file path?

ADD REPLY •

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