Question

ChIPQC error: "non-zero exit status"

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hallie.s • 0

@hallies-16494

Last seen 6.4 years ago

Hi,

I am following a ChIP-seq data analysis practical guide that requires me to use the packages ChIPQC, GenomicAlignments, and GenomicRanges. I am not having any trouble with the last two packages, however I cannot install the ChIPQC package. I have tried to install the package using library(biocInstaller), and then biocLite("ChIPQC"), but I get an error from R stating the package had a "non-zero exit status." I don't know what the error means or how to fix it. Does anyone know what this means exactly or what I can do to try to resolve the issue? Is it possible that the package is dependent on other packages which may be incompatible with my version of R (3.5.0)? Or is there a chance that there is a "bug" in my code/R/other that I'm unaware of which may be interfering with my ability to install and load the package?

(The code below is just part of the error that I got)

Any suggestions would be greatly appreciated, thanks!

biocLite("ChIPQC")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).

Installing package(s) ‘ChIPQC’

also installing the dependencies ‘TxDb.Hsapiens.UCSC.hg18.knownGene’, ‘TxDb.Mmusculus.UCSC.mm10.knownGene’, ‘TxDb.Mmusculus.UCSC.mm9.knownGene’, ‘TxDb.Rnorvegicus.UCSC.rn4.ensGene’, ‘TxDb.Celegans.UCSC.ce6.ensGene’, ‘TxDb.Dmelanogaster.UCSC.dm3.ensGene’

trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/ChIPQC_1.16.0.zip'

Content type 'application/zip' length 2017947 bytes (1.9 MB)

downloaded 1.9 MB

package ‘ChIPQC’ successfully unpacked and MD5 sums checked

trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz'

Content type 'application/x-gzip' length 4588884 bytes (4.4 MB)

downloaded 4.4 MB

* installing *source* package 'TxDb.Hsapiens.UCSC.hg18.knownGene' ...

** R

** inst

** byte-compile and prepare package for lazy loading

Error: package or namespace load failed for 'GenomeInfoDb' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

there is no package called 'RCurl'

Error : package 'GenomeInfoDb' could not be loaded

ERROR: lazy loading failed for package 'TxDb.Hsapiens.UCSC.hg18.knownGene'

Warning messages:

1: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘TxDb.Hsapiens.UCSC.hg18.knownGene’ had non-zero exit status

2: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘TxDb.Mmusculus.UCSC.mm10.knownGene’ had non-zero exit status

3: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘TxDb.Mmusculus.UCSC.mm9.knownGene’ had non-zero exit status

4: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘TxDb.Rnorvegicus.UCSC.rn4.ensGene’ had non-zero exit status

5: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘TxDb.Celegans.UCSC.ce6.ensGene’ had non-zero exit status

6: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘TxDb.Dmelanogaster.UCSC.dm3.ensGene’ had non-zero exit status

software error package installation chipqc txdb.hsapiens.ucsc.hg18.knowngene • 2.5k views

ADD COMMENT • link updated 6.4 years ago by Martin Morgan 25k • written 6.4 years ago by hallie.s • 0

0

Entering edit mode

Could you post your session information so we can see which versions of libraries you currently have installed?

best,

tom

ADD REPLY • link 6.4 years ago Thomas Carroll ▴ 420

score 0 · Answer 1 · 2018-07-16

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Martin Morgan 25k

@martin-morgan-1513

Last seen 5 months ago

United States

Tackle the first error that is reported

there is no package called 'RCurl'

and debug that first -- what happens with

BiocInstaller::biocLite("RCurl")

?

ADD COMMENT • link 6.4 years ago Martin Morgan 25k

0

Entering edit mode

I think the installation of RCurl worked, but I tried running the code that I need again and it still doesn't seem to be working. Also, the errors that I receive say that I don't have certain packages installed even though I do have them installed (they show up in my packages list in my library).

> library(GenomicAlignments) Loading required package: GenomeInfoDb Loading required package: GenomicRanges package �GenomicRanges� was built under R version 3.5.1Loading required package: SummarizedExperiment Loading required package: DelayedArray Loading required package: matrixStats Attaching package: �matrixStats� The following objects are masked from �package:Biobase�: anyMissing, rowMedians Loading required package: BiocParallel package �BiocParallel� was built under R version 3.5.1 Attaching package: �DelayedArray� The following objects are masked from �package:matrixStats�: colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following object is masked from �package:Biostrings�: type The following objects are masked from �package:base�: aperm, apply Loading required package: Rsamtools package �Rsamtools� was built under R version 3.5.1 > library(ChIPQC) Loading required package: ggplot2 package �ggplot2� was built under R version 3.5.1Loading required package: DiffBind Error: package or namespace load failed for �DiffBind� in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called �stringi� Error: package ‘DiffBind’ could not be loaded

After this error appeared, I tried to install "DiffBind." However, even after installing DiffBind and running the code again to load ChIPQC library, I get the same error that says "DiffBind could not be loaded."

> BiocInstaller::biocLite("DiffBind") BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23). Installing package(s) ‘DiffBind’ trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/DiffBind_2.8.0.zip' Content type 'application/zip' length 3064647 bytes (2.9 MB) downloaded 2.9 MB package ‘DiffBind’ successfully unpacked and MD5 sums checked

Old packages: 'RCurl', 'XML' Update all/some/none? [a/s/n]: a There are binary versions available but the source versions are later: binary source needs_compilation

RCurl 1.95-4.10 1.95-4.11 TRUE

XML 3.98-1.11 3.98-1.12 TRUE

Binaries will be installed trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/RCurl_1.95-4.10.zip' Content type 'application/zip' length 2969339 bytes (2.8 MB) downloaded 2.8 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/XML_3.98-1.11.zip' Content type 'application/zip' length 4601014 bytes (4.4 MB) downloaded 4.4 MB package ‘RCurl’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘RCurl’ package ‘XML’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘XML’

ADD REPLY • link 6.4 years ago hallie.s • 0

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Entering edit mode

Error: package or namespace load failed for �DiffBind� in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called �stringi�
Error: package ‘DiffBind’ could not be loaded

Although DiffBind could not be loaded, the reason is because 'there is no package called "stringi"', so you must install stringi. I'm not sure why you are having to install these individual packages, usually when you install a package for the first time, all of its dependencies are installed.

Also, I would recommend saying 'n' to updating RCurl and XML -- probably the 'new' versions are the 'source' versions, and you do not have the software on your computer to install the source versions.

Finally,

Warning: cannot remove prior installation of package ‘RCurl

means that RCurl and XML are already in use in your R session, or in another R session on your computer; the best practice is to install packages in a new R session.

ADD REPLY • link 6.4 years ago Martin Morgan 25k