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mdroog
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@mdroog-13422
Last seen 5.4 years ago
Yesterday I managed to install DESeq2 on my home computer but today it simply won't work on my computer at work.
I install it using the following command:
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
However, when I then use the command
library(DESeq2)
I get the following:
> library(DESeq2) Loading required package: GenomicRanges Loading required package: GenomeInfoDb Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘GenomeInfoDbData’ Error: package ‘GenomeInfoDb’ could not be loaded
And so I installed GenomicRanges and GenomeInfoDb using biocLite, but I keep getting this error message.
What should I change?
> sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] Biobase_2.36.2 edgeR_3.18.1 limma_3.32.2 BiocInstaller_1.26.0 IRanges_2.10.2 [6] S4Vectors_0.14.3 BiocGenerics_0.22.0 loaded via a namespace (and not attached): [1] compiler_3.4.1 tools_3.4.1 RCurl_1.95-4.8 grid_3.4.1 locfit_1.5-9.1 bitops_1.0-6 lattice_0.20-35 |
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I did but then I get the following messages: > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help > biocLite("GenomeInfoDb") BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.1 (2017-06-30). Installing package(s) ‘GenomeInfoDb’ also installing the dependency ‘GenomeInfoDbData’ trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/GenomeInfoDb_1.12.2.zip' Content type 'application/zip' length 7073643 bytes (6.7 MB) downloaded 6.7 MB package ‘GenomeInfoDb’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\m.droog\AppData\Local\Temp\Rtmp4Yo5FY\downloaded_packages installing the source package ‘GenomeInfoDbData’ trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz' Content type 'application/x-gzip' length 16238792 bytes (15.5 MB) downloaded 15.5 MB '\\srv-data1\home$\M87E6~1.DRO\R\R-34~1.1' is not recognized as an internal or external command, operable program or batch file. The downloaded source packages are in ‘C:\Users\m.droog\AppData\Local\Temp\Rtmp4Yo5FY\downloaded_packages’ Old packages: 'Formula', 'scater' Update all/some/none? [a/s/n]: a There are binary versions available but the source versions are later: binary source needs_compilation Formula 1.2-1 1.2-2 FALSE scater 1.3.35 1.4.0 TRUE Binaries will be installed trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/scater_1.3.35.zip' Content type 'application/zip' length 7883976 bytes (7.5 MB) downloaded 7.5 MB package ‘scater’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\m.droog\AppData\Local\Temp\Rtmp4Yo5FY\downloaded_packages installing the source package ‘Formula’ trying URL 'https://cran.rstudio.com/src/contrib/Formula_1.2-2.tar.gz' Content type 'application/x-gzip' length 150946 bytes (147 KB) downloaded 147 KB '\\srv-data1\home$\M87E6~1.DRO\R\R-34~1.1' is not recognized as an internal or external command, operable program or batch file. The downloaded source packages are in ‘C:\Users\m.droog\AppData\Local\Temp\Rtmp4Yo5FY\downloaded_packages’ Warning messages: 1: running command '"//srv-data1/home$/M87E6~1.DRO/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "\\srv-data1\home$\m.droog\R\R-3.4.1\library" C:\Users\M87E6~1.DRO\AppData\Local\Temp\Rtmp4Yo5FY/downloaded_packages/GenomeInfoDbData_0.99.0.tar.gz' had status 1 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘GenomeInfoDbData’ had non-zero exit status 3: running command '"//srv-data1/home$/M87E6~1.DRO/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "\\srv-data1\home$\m.droog\R\R-3.4.1\library" C:\Users\M87E6~1.DRO\AppData\Local\Temp\Rtmp4Yo5FY/downloaded_packages/Formula_1.2-2.tar.gz' had status 1 4: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘Formula’ had non-zero exit status > library(GenomeInfoDb) Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘GenomeInfoDbData’R does not like the 'network' file path "
\\srv-data1\home$\m.droog..."; google for 'map network drive' to associate this path with a letter, so that the path is "z:\...".Yes, thank you. That was it indeed. Instead of the network drive, R is now running on the local D:\\ disk. This solved the problem.
Hi!!
I am having this same problem you had. How you solved it?
Thanks in advance!!!
Ida
Did you not see the comment you replied to (where the OP said it was fixed) and the previous comment (where Martin told the OP how to fix it)?
I did and I got this other error:
> biocLite(c("GenomeInfoDb")) BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02). Installing package(s) ‘GenomeInfoDb’ also installing the dependency ‘GenomeInfoDbData’ trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/GenomeInfoDb_1.16.0.zip' Content type 'application/zip' length 3830739 bytes (3.7 MB) downloaded 3.7 MB package ‘GenomeInfoDb’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\Ida.G.PantojaFelicia\AppData\Local\Temp\RtmpOyhiyI\downloaded_packages installing the source package ‘GenomeInfoDbData’ trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz' Content type 'application/x-gzip' length 8204728 bytes (7.8 MB) downloaded 7.8 MB '\\natia7ndenas2\DPS\IDAG~1.PAN\DOCUME~1\R\R-35~1.1' is not recognized as an internal or external command, operable program or batch file. In R CMD INSTALL The downloaded source packages are in ‘C:\Users\Ida.G.PantojaFelicia\AppData\Local\Temp\RtmpOyhiyI\downloaded_packages’ Old packages: 'R6', 'rstudioapi', 'stringi' Update all/some/none? [a/s/n]: a There are binary versions available but the source versions are later: binary source needs_compilation R6 2.2.2 2.3.0 FALSE rstudioapi 0.7 0.8 FALSE stringi 1.1.7 1.2.4 TRUE Binaries will be installed trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/stringi_1.1.7.zip' Content type 'application/zip' length 14368013 bytes (13.7 MB) downloaded 13.7 MB package ‘stringi’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\Ida.G.PantojaFelicia\AppData\Local\Temp\RtmpOyhiyI\downloaded_packages installing the source packages ‘R6’, ‘rstudioapi’ trying URL 'https://cran.rstudio.com/src/contrib/R6_2.3.0.tar.gz' Content type 'application/x-gzip' length 30968 bytes (30 KB) downloaded 30 KB trying URL 'https://cran.rstudio.com/src/contrib/rstudioapi_0.8.tar.gz' Content type 'application/x-gzip' length 47394 bytes (46 KB) downloaded 46 KB '\\natia7ndenas2\DPS\IDAG~1.PAN\DOCUME~1\R\R-35~1.1' is not recognized as an internal or external command, operable program or batch file. In R CMD INSTALL '\\natia7ndenas2\DPS\IDAG~1.PAN\DOCUME~1\R\R-35~1.1' is not recognized as an internal or external command, operable program or batch file. In R CMD INSTALL The downloaded source packages are in ‘C:\Users\Ida.G.PantojaFelicia\AppData\Local\Temp\RtmpOyhiyI\downloaded_packages’ Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘GenomeInfoDbData’ had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘R6’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘rstudioapi’ had non-zero exit statusExactly. And what did Martin say you should do in order to fix that?
Look, I did the 'map network drive' and I am still getting that error I just posted.
Evidently it didn't work, because R is still trying to install to the network drive rather than the mapping you say you set up.
The troublesome looking line in your output is
What does
R.home()report? It should have the mapped network drive, with a form like W:\\...Hi Martin,
Thanks so much for your response.
This is what I get when I do R.home():
I am in a Government Computer and I am not sure if I am having some restrictions. When I did the google search for map network drive and followed the steps, I selected the letter but in the Folder Section, Browse, I only see one option for Network. I can't select any other Folder because is empty. Otherwise, I typed the path in the space provided for "Folder". It created a mapped network drive because I see it under My PC but when I run again the command, does not work. It is not connecting the letter. That's why I think there are some restrictions and I have to contact IT people. But I could be wrong and there is some step I am not doing.
Thanks again!
Ida
It is not unreasonable to ask your local help desk to support you in this.