Entering edit mode
@cristoforo-grasso-16658
Last seen 7.3 years ago
I am a beginner user of R and the Biocunductor packages. I am analysing RNA seq data, amang many pakages that I have installed thare is the Delayedarray package, of which I am having trouble to install. The output is a warning message. I wonder if you coud help me. Thank you in advance
There is a binary version available but the source version is later:
binary source needs_compilation
matrixStats 0.53.1 0.54.0 TRUE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/matrixStats_0.53.1.zip'
Content type 'application/zip' length 1632527 bytes (1.6 MB)
downloaded 1.6 MB
package ‘matrixStats’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\cgrasso\AppData\Local\Temp\RtmpkfIVn0\downloaded_packages
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘DelayedArray’ had non-zero exit status
> BiocInstaller::biocValid()
* sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252
[3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C
[5] LC_TIME=Dutch_Netherlands.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BiocInstaller_1.30.0 Biobase_2.40.0 Rsamtools_1.32.2
[4] GenomicRanges_1.32.6 GenomeInfoDb_1.16.0 Biostrings_2.48.0
[7] XVector_0.20.0 IRanges_2.14.10 S4Vectors_0.18.3
[10] BiocParallel_1.14.2 BiocGenerics_0.26.0
loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(X[[i]], ...) :
DESCRIPTION file of package 'yaml' is missing or broken
> traceback()
10: FUN(X[[i]], ...)
9: lapply(X = X, FUN = FUN, ...)
8: sapply(L[[n]], function(x) x[["Version"]])
7: mkLabel(x, "loadedOnly")
6: print(mkLabel(x, "loadedOnly"), quote = FALSE, ...)
5: print.sessionInfo(sessionInfo())
4: print(sessionInfo())
3: print.biocValid(result)
2: print(result)
1: BiocInstaller::biocValid()
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252
[3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C
[5] LC_TIME=Dutch_Netherlands.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BiocInstaller_1.30.0 Biobase_2.40.0 Rsamtools_1.32.2
[4] GenomicRanges_1.32.6 GenomeInfoDb_1.16.0 Biostrings_2.48.0
[7] XVector_0.20.0 IRanges_2.14.10 S4Vectors_0.18.3
[10] BiocParallel_1.14.2 BiocGenerics_0.26.0
loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(X[[i]], ...) :
DESCRIPTION file of package 'yaml' is missing or broken

To clarify, was this using
BiocInstaller::biocLite("DelayedArray")?