I'm very new to R and I'm running into the same problem over and over again. I tried already all solution suggestions I could find but nothing is working.
I try to install the BSgenome.Hsapiens:UCSC.hg19 using
BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
and I'll always get the same error warning.
BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'BSgenome.Hsapiens.UCSC.hg19'
installing the source package ‘BSgenome.Hsapiens.UCSC.hg19’
versuche URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz'
Content type 'application/x-gzip' length 688190187 bytes (656.3 MB)
downloaded 656.3 MB
"\\"
CMD.EXE wurde mit dem oben angegebenen Pfad als aktuellem Verzeichnis gestartet.
UNC-Pfade werden nicht untersttzt.
Stattdessen wird das Windows-Verzeichnis als aktuelles Verzeichnis gesetzt.
* installing *source* package 'BSgenome.Hsapiens.UCSC.hg19' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Fehler in findpack(package, lib.loc) :
there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
Ruft auf: <Anonymous> -> findpack
Ausführung angehalten
ERROR: lazy loading failed for package 'BSgenome.Hsapiens.UCSC.hg19'
* removing '\\'
The downloaded source packages are in
‘C:\Users\montag\AppData\Local\Temp\Rtmpo3Vm0w\downloaded_packages’
Installation path not writeable, unable to update packages: boot, foreign, KernSmooth, Matrix, mgcv, nlme, survival
Old packages: 'cli', 'plyr'
Update all/some/none? [a/s/n]:
a
There are binary versions available but the source versions are later:
binary source needs_compilation
cli 1.1.0 2.0.0 FALSE
plyr 1.8.4 1.8.5 TRUE
Binaries will be installed
versuche URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/plyr_1.8.4.zip'
Content type 'application/zip' length 1302229 bytes (1.2 MB)
downloaded 1.2 MB
package ‘plyr’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\montag\AppData\Local\Temp\Rtmpo3Vm0w\downloaded_packages
installing the source package ‘cli’
versuche URL 'https://cran.rstudio.com/src/contrib/cli_2.0.0.tar.gz'
Content type 'application/x-gzip' length 111873 bytes (109 KB)
downloaded 109 KB
"\\"
CMD.EXE wurde mit dem oben angegebenen Pfad als aktuellem Verzeichnis gestartet.
UNC-Pfade werden nicht untersttzt.
Stattdessen wird das Windows-Verzeichnis als aktuelles Verzeichnis gesetzt.
* installing *source* package 'cli' ...
** Paket 'cli' erfolgreich entpackt und MD5 Summen überprüft
ERROR: cannot remove earlier installation, is it in use?
* removing '\\'
* restoring previous '\\'
The downloaded source packages are in
‘C:\Users\montag\AppData\Local\Temp\Rtmpo3Vm0w\downloaded_packages’
Warnmeldungen:
1: In install.packages(...) :
installation of package ‘BSgenome.Hsapiens.UCSC.hg19’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘cli’ had non-zero exit status
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C LC_TIME=German_Germany.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome_1.54.0 rtracklayer_1.46.0 Biostrings_2.54.0 XVector_0.26.0 GenomicRanges_1.38.0
[6] GenomeInfoDb_1.22.0 IRanges_2.20.1 S4Vectors_0.24.1 BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] zlibbioc_1.32.0 GenomicAlignments_1.22.1 BiocParallel_1.20.0 lattice_0.20-38
[5] tools_3.6.1 SummarizedExperiment_1.16.0 grid_3.6.1 Biobase_2.46.0
[9] matrixStats_0.55.0 Matrix_1.2-17 GenomeInfoDbData_1.2.2 BiocManager_1.30.10
[13] bitops_1.0-6 RCurl_1.95-4.12 DelayedArray_0.12.0 compiler_3.6.1
[17] Rsamtools_2.2.1 XML_3.98-1.20
Please help me, I'm desperate at the moment
Hi,
I see "Installation path not writeable" in the error messages you're showing us so I wonder: Can you install any package at all? Try something like:
If this fails then your problem does not have much to do with the BSgenome.Hsapiens.UCSC.hg19 package or with Bioconductor. It's about your R setup which seems broken and would need to be fixed first.
H.
No installation is not my general problem. I can install packages and load them. But everything related to Bioconductor seems to be the Problem. I also get the same error when trying to install Homo.sapiens
Update: I found a way to install both packages with the help of further research. See further down for details