Entering edit mode
Guido Hooiveld
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@guido-hooiveld-2020
Last seen 3 hours ago
Wageningen University, Wageningen, the …
I face an error when installing the PdInfo package pd.huex.1.0.st.v2 (required to use some sample data for oligo [package oligoData]). The returned error is "database disk image is malformed
". Any idea what may go wrong?
> source("https://bioconductor.org/biocLite.R") Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help > biocLite("pd.huex.1.0.st.v2") BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 Patched (2017-05-10 r72670). Installing package(s) ‘pd.huex.1.0.st.v2’ installing the source package ‘pd.huex.1.0.st.v2’ trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/pd.huex.1.0.st.v2_3.14.1.tar.gz' Content type 'application/x-gzip' length 314073786 bytes (299.5 MB) downloaded 299.5 MB * installing *source* package 'pd.huex.1.0.st.v2' ... ** R ** data ** inst ** preparing package for lazy loading Warning: package 'Biostrings' was built under R version 3.4.1 No methods found in "RSQLite" for requests: dbGetQuery Warning: package 'oligo' was built under R version 3.4.1 Warning: Couldn't set synchronous mode: database disk image is malformed Use `synchronous` = NULL to turn off this warning. Error in rsqlite_send_query(conn@ptr, statement) : database disk image is malformed Error : unable to load R code in package 'pd.huex.1.0.st.v2' ERROR: lazy loading failed for package 'pd.huex.1.0.st.v2' * removing 'C:/Program Files/R/R-3.4.0patched/library/pd.huex.1.0.st.v2' The downloaded source packages are in ‘D:\TMP\RtmpiSXYou\downloaded_packages’ Warning messages: 1: running command '"C:/PROGRA~1/R/R-34~1.0PA/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.4.0patched\library" D:\TMP\ RtmpiSXYou/downloaded_packages/pd.huex.1.0.st.v2_3.14.1.tar.gz' had status 1 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘pd.huex.1.0.st.v2’ had non-zero exit status >
> sessionInfo() R version 3.4.0 Patched (2017-05-10 r72670) 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=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.26.0 loaded via a namespace (and not attached): [1] compiler_3.4.0 tools_3.4.0 >
Re-installing did not solve the problem. (I already did try so before posting, but forgot to add that to my question; sorry).
Seems OK to me?
Mmm, something weird is going on...
- I freshly installed (updated R to) R-3.4.1 (same as you, I was running R-3.4.0), and re-installed the latest RTools, but problem unfortunately remained...?
- To exclude it may have something to do with relatively large size of the PdInfo package, I tried to install a smaller variant (
pd.hg.u133.plus.2
) to avoid problems with downloading/disc size, etc. Again, this didn't work; messageNo methods found in "RSQLite" for requests: dbGetQuery
also appeared.- After some Googling I found your post A: RSQLite reverse dependencies Same error, similar situation in the sense you mentioned
oligoClasses
. Despite the fact I run the same R/libraries as you (sessionInfo), could this somehow be the culprit?<<EDIT>> I just noticed that the message
No methods...
. also popped up in your session. Apparently this is a warning, and not a (fatal) error, because I indeed could load the PdInfo package without problems (library("pd.hg.u133.plus.2")
). I was too focused on all these messages, and didn't realize this was NOT related to my original problem... Sorry for the confusion... !<<EDIT2>> Installing and loading
pd.huex.1.0.st.v2
also went fine (thoughNo methods
message is returned).Nice. And yes, the warning is just pointing out something that is fixed in the devel version of Bioconductor, but I didn't push a fix to release since it's a warning, not a bug.