Question: ChIPQC error: "non-zero exit status"
0
gravatar for hallie.s
11 months ago by
hallie.s0
hallie.s0 wrote:

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

ADD COMMENTlink modified 11 months ago by Martin Morgan ♦♦ 23k • written 11 months ago by hallie.s0

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

best,

tom

ADD REPLYlink written 11 months ago by Thomas Carroll400
Answer: ChIPQC error: "non-zero exit status"
0
gravatar for Martin Morgan
11 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Tackle the first error that is reported

there is no package called 'RCurl'

and debug that first -- what happens with

BiocInstaller::biocLite("RCurl")

?

ADD COMMENTlink written 11 months ago by Martin Morgan ♦♦ 23k

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 REPLYlink written 11 months ago by hallie.s0
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 REPLYlink written 11 months ago by Martin Morgan ♦♦ 23k
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