Question: Problem in installing maEndToEnd package
0
gravatar for truong128
15 days ago by
truong1280
truong1280 wrote:

Dear Bioconductor admin,

I am Truong Nguyen

I am working on data analysis for microarray data, but I could not install into my R studio,

Could you please help me solve my issue that How to install "maEndToEnd" into R studio in my Macbook?

Thank you very much Sincerely

Here is the problem report from my screen:

> library(devtools)
> library(remotes)
> remotes::install_github("b-klaus/maEndToEnd", ref="master")
Downloading GitHub repo b-klaus/maEndToEnd@master
Skipping 42 packages ahead of CRAN: Biobase, oligoClasses, ArrayExpress, oligo, arrayQualityMetrics, limma, topGO, ReactomePA, clusterProfiler, geneplotter, genefilter, Rgraphviz, BiocGenerics, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, affyio, S4Vectors, AnnotationDbi, affxparser, preprocessCore, zlibbioc, affy, affyPLM, beadarray, vsn, graph, DOSE, enrichplot, graphite, GOSemSim, qvalue, annotate, GenomeInfoDb, XVector, DelayedArray, BiocParallel, gcrma, BeadDataPackR, illuminaio, fgsea
✔  checking for file ‘/private/var/folders/cy/rq7bxr0d7zx2vdh77jwng_4h0000gn/T/RtmpnI7Ct0/remotes19294101919d/b-klaus-maEndToEnd-2e5cae5/DESCRIPTION’ (411ms)
─  preparing ‘maEndToEnd’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘maEndToEnd_1.99.6.tar.gz’

* installing *source* package ‘maEndToEnd’ ...
** using staged installation
** inst
** help
No man pages found in package  ‘maEndToEnd’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘arrayQualityMetrics’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so, 6): Library not loaded: /opt/X11/lib/libcairo.2.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so
  Reason: image not found
Error : package ‘arrayQualityMetrics’ could not be loaded
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/maEndToEnd’
Error: Failed to install 'maEndToEnd' from GitHub:
  (converted from warning) installation of package ‘/var/folders/cy/rq7bxr0d7zx2vdh77jwng_4h0000gn/T//RtmpnI7Ct0/file19294dfefbc2/maEndToEnd_1.99.6.tar.gz’ had non-zero exit status
microarray maendtoend • 62 views
ADD COMMENTlink written 15 days ago by truong1280

Could you try installing from Bioconductor

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# If you want the development versions of packages: 
BiocManager::install(version='devel')

BiocManager::install("maEndToEnd")

You could also check the installation of packages to make sure dependencies are up to date:

BiocManager::valid()
ADD REPLYlink modified 15 days ago • written 15 days ago by shepherl ♦♦ 1.4k

I did try that method with many many times but it still showed the same problem, Could you please try with your Mac? I think this package has serious problem in installing

Thanks a lot

ADD REPLYlink written 14 days ago by truong1280

it still show

  • installing source package ‘maEndToEnd’ ... * using staged installation * inst * help No man pages found in package ‘maEndToEnd’ ** installing help indices * building package indices * installing vignettes ** testing if installed package can be loaded from temporary location
ADD REPLYlink written 14 days ago by truong1280
Answer: C: Problem in installing maEndToEnd package
1
gravatar for shepherl
14 days ago by
shepherl ♦♦ 1.4k
United States
shepherl ♦♦ 1.4k wrote:

The ERROR messages above are actually coming from arrayQualityMetrics package not being able to install. It looks like it actually has to do with system dependencies.

From some other packages that were having similar issues the suggestion is to reinstall XQuartz at https://www.xquartz.org/ and possibly a reinstall of cairo. (references: https://github.com/thomasp85/gganimate/issues/95 and https://github.com/davidgohel/gdtools/issues/43#issuecomment-375056815)

Could you please do a system reinstall of XQuartz and try installing in R arrayQualityMetrics. BiocManager::install("arrayQualityMetrics") and if those are successful then try maEndToEnd again.

ADD COMMENTlink modified 14 days ago • written 14 days ago by shepherl ♦♦ 1.4k

Awesome,

Thank you very much Shepherl,

It works perfectly now,

ADD REPLYlink written 14 days ago by truong1280
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