GenomeInfoDbData had non-zero exit status
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JoseR • 0
@8adb064e
Last seen 2.4 years ago
Spain

Hello! I know this is a post closely related with others posted here. However, I have not been able to fix this issue with that information. I am running RStudio with R 4.2.1 in windows10 and I am trying to install the DEseq2 package using the recommended commands:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager") BiocManager::install("DESeq2")

All commands run well, however, at the end of the installation the next problem related with GenomeInfoDbData pops up:

The downloaded binary packages are in
    C:\Users\joser\AppData\Local\Temp\Rtmpw7QBW1\downloaded_packages
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GenomeInfoDbData_1.2.8.tar.gz'
Content type 'application/x-gzip' length 11512907 bytes (11.0 MB)
downloaded 11.0 MB


The downloaded source packages are in
    ‘C:\Users\joser\AppData\Local\Temp\Rtmpw7QBW1\downloaded_packages’
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.2.1/library
  packages:
    nlme
Warning message:
In install.packages(...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status

I have tried to solve this problem in different ways (re-installing R and Rstudio several times and removing old files, installing GenomeInfoDbData alone using BiocManager and from source, with and without admin permissions...) but all failed and all finally reported "installation of package ‘GenomeInfoDbData’ had non-zero exit status". Do you have any clue about what could be going on here?

Many thanks!
DESeq2 RStudio GenomeInfoDbData hadnon-zeroexitstatus • 5.0k views
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An update, I have noticed that when installing DESeq2 with BiocManager, the only library that fails is always GenomeInfoDbData an also is the unique package that is tar.gz compressed. I don´t know if that could be the source of the problem... I have tried to uncompress and re-compress in zip but it is also not working...

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@mikelove
Last seen 4 days ago
United States

Try to say no to updating packages, and no to installing from source, when prompted.
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Thanks for your reply. I have try it, but it remains the same.

> BiocManager::install("GenomeInfoDbData", ask = TRUE, update = FALSE)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Installing package(s) 'GenomeInfoDbData'
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GenomeInfoDbData_1.2.8.tar.gz'
Content type 'application/x-gzip' length 11512907 bytes (11.0 MB)
downloaded 11.0 MB


The downloaded source packages are in
    ‘C:\Users\joser\AppData\Local\Temp\Rtmpg59WZ3\downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status
>
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GenomeInfoDb has a 64 bit binary, I'm not sure why it's not installing for you:

https://bioconductor.org/packages/release/bioc/html/GenomeInfoDb.html

Are you not on a 64 bit machine?

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Yes, it is a 64 bit (x64) machine:

R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit)

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I don’t know why it would install from source unless you say [y] when prompted. But the binary is available on the website you could just download it and install the binary from your local machine.

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I have tried installing GenomeInfoDb, but it comes with the same GenomeInfoDbData error. I have try to install GenomeInfoDbData from binary, but there is no any Windows Binary in the Bioconductor page (https://bioconductor.org/packages/release/data/annotation/html/GenomeInfoDbData.html).

> install.packages("C:/Users/joser/Downloads/GenomeInfoDb_1.32.2.zip", repos = NULL, type = "win.binary")
Installing package into ‘C:/Users/joser/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
package ‘GenomeInfoDb’ successfully unpacked and MD5 sums checked
> library("GenomeInfoDb")
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame,
    basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, Filter, Find, get,
    grep, grepl, intersect, is.unsorted, lapply,
    Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff,
    sort, table, tapply, union, unique, unsplit,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:grDevices’:

    windows

Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GenomeInfoDbData’

Regardless to the "I don’t know why it would install from source unless you say [y] when prompted" It is not giving me the option to answer in the prompt. It just try to install it without asking me:

> BiocManager::install("GenomeInfoDbData")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Installing package(s) 'GenomeInfoDbData'
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GenomeInfoDbData_1.2.8.tar.gz'
Content type 'application/x-gzip' length 11512907 bytes (11.0 MB)
downloaded 11.0 MB


The downloaded source packages are in
    ‘C:\Users\joser\AppData\Local\Temp\RtmpobqssT\downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status
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GenomeInfoDbData is an annotation package, so there are no binaries. All you can get is the source package. I can't get the same error as you, so it's unclear what the problem is. What do you get from

dir(.libPaths()[1], "Genome")

If that returns 'GenomeInfoDbData' as one of the results, then you might try

z <-  dir(.libPaths()[1], "Genome", full.names = TRUE)
z <- z[grep("GenomeInfoDbData", z)]
unlink(z, recursive = TRUE)
install("GenomeInfoDbData")

And see if that helps.

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No, it only returns GenomeInfoDB.

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Is the output you provided the entirety of the output or have you subsetted? I get much more

> install("GenomeInfoDbData", force = TRUE)
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22 ucrt)
Installing package(s) 'GenomeInfoDbData'
installing the source package 'GenomeInfoDbData'

trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GenomeInfoDbData_1.2.8.tar.gz'
Content type 'application/x-gzip' length 11512907 bytes (11.0 MB)
downloaded 11.0 MB

* installing *source* package 'GenomeInfoDbData' ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDbData)

The downloaded source packages are in
    'C:\Users\Public\Documents\Wondershare\CreatorTemp\RtmpY78tX0\downloaded_packages'
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Yes, it is the full output. Here is what happend when I don´t update:

> install("GenomeInfoDbData", force = TRUE)
'getOption("repos")' replaces Bioconductor
standard repositories, see '?repositories' for
details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R
  4.2.1 (2022-06-23 ucrt)
Installing package(s) 'GenomeInfoDbData'
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GenomeInfoDbData_1.2.8.tar.gz'
Content type 'application/x-gzip' length 11512907 bytes (11.0 MB)
downloaded 11.0 MB


The downloaded source packages are in
    ‘C:\Users\joser\AppData\Local\Temp\RtmpsF3cDn\downloaded_packages’
Installation paths not writeable, unable to update
  packages
  path: C:/Program Files/R/R-4.2.1/library
  packages:
    nlme
Old packages: 'rlang'
Update all/some/none? [a/s/n]: 
n
Warning message:
In install.packages(...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status

It is indicating that the package 'rlang' is an old version, so I have tried to re-install it, but it is also saying the non-zero exit status for this package. Could it be a problem when installing from source?


> install.packages("rlang", force = TRUE)
Installing package into ‘C:/Users/joser/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)

  There is a binary version available but the source version is later:
      binary source needs_compilation
rlang  1.0.3  1.0.4              TRUE

installing the source package ‘rlang’

trying URL 'https://cran.rstudio.com/src/contrib/rlang_1.0.4.tar.gz'
Content type 'application/x-gzip' length 740971 bytes (723 KB)
downloaded 723 KB

Warning in install.packages :
  installation of package ‘rlang’ had non-zero exit status
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There are two main types of source packages. Those that have code that needs to be compiled, and those that do not. For the former you need to have a toolchain that is capable of doing the compilation, and on Windows for R it's the RTools package. I don't believe it's necessary to have RTools installed for the data packages. But it is necessary for rlang (the gcc and g++ lines below are linking/compiling of C++ code).

> install("rlang", force = TRUE, type = "source")
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22 ucrt)
Installing package(s) 'rlang'
trying URL 'https://cloud.r-project.org/src/contrib/rlang_1.0.4.tar.gz'
Content type 'application/x-gzip' length 740971 bytes (723 KB)
downloaded 723 KB

* installing *source* package 'rlang' ...
** package 'rlang' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc  -I"c:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c capture.c -o capture.o
gcc  -I"c:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c internal.c -o internal.o
g++  -std=gnu++11 -I"c:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rlang-rcc.cpp -o rlang-rcc.o
gcc  -I"c:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rlang.c -o rlang.o
gcc  -I"c:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I./rlang/    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c version.c -o version.o
g++ -shared -s -static-libgcc -o rlang.dll tmp.def capture.o internal.o rlang-rcc.o rlang.o version.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -Lc:/PROGRA~1/R/R-42~1.0/bin/x64 -lR
installing to C:/Users/jmacdon/AppData/Local/R/win-library/4.2/00LOCK-rlang/00new/rlang/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rlang)

Maybe try installing Rtools and see if that helps with GenomeInfoDbData? I don't think that's the issue, but while we're grasping at straws...

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I already had installed Rtools. and I have tried again, now I have another "Old package" issue:

> if (!require("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
> install("rlang", force = TRUE, type = "source")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Installing package(s) 'rlang'
trying URL 'https://cran.rstudio.com/src/contrib/rlang_1.0.4.tar.gz'
Content type 'application/x-gzip' length 740971 bytes (723 KB)
downloaded 723 KB


The downloaded source packages are in
    ‘C:\Users\joser\AppData\Local\Temp\RtmpSiwcef\downloaded_packages’
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.2.1/library
  packages:
    nlme
Old packages: 'KEGGREST', 'rlang'
Update all/some/none? [a/s/n]: 
a
trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/KEGGREST_1.36.3.tar.gz'
Content type 'application/x-gzip' length 25794 bytes (25 KB)
downloaded 25 KB

trying URL 'https://cran.rstudio.com/src/contrib/rlang_1.0.4.tar.gz'
Content type 'application/x-gzip' length 740971 bytes (723 KB)
downloaded 723 KB


The downloaded source packages are in
    ‘C:\Users\joser\AppData\Local\Temp\RtmpSiwcef\downloaded_packages’
Warning messages:
1: In install.packages(...) :
  installation of package ‘rlang’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘KEGGREST’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘rlang’ had non-zero exit status

I am starting to think about a bigger problem of my windows system because the cmd console is not working anymore also and maybe both problems are related somehow. Maybe some corrupted system file I guess, so I will carry out a system restore...

Thank you James and Michael for helping me with this. I will report here If I solve the problem with this drastic solution.

Cheers.

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Did you ever find a solution @JoseR? I have been experiencing the same non-zero exit status issue on R 4.2.1.

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