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Question: Error installing pd.huex.1.0.st.v2: database disk image is malformed
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gravatar for Guido Hooiveld
3 months ago by
Guido Hooiveld2.2k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.2k wrote:

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   
>

 

ADD COMMENTlink modified 3 months ago by James W. MacDonald45k • written 3 months ago by Guido Hooiveld2.2k
2
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald45k wrote:

That error seems to imply that the underlying database for this package is corrupted. Try re-installing.

ADD COMMENTlink written 3 months ago by James W. MacDonald45k

Re-installing did not solve the problem. (I already did try so before posting, but forgot to add that to my question; sorry).

ADD REPLYlink written 3 months ago by Guido Hooiveld2.2k
2

Seems OK to me?

> biocLite("pd.huex.1.0.st.v2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.1 (2017-06-30).
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
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
No methods found in "RSQLite" for requests: dbGetQuery
*** arch - x64
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (pd.huex.1.0.st.v2)

The downloaded source packages are in
    'C:\Users\Public\Documents\Wondershare\CreatorTemp\Rtmp8MvMdW\downloaded_packages'

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

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_3.4.1 tools_3.4.1   
>
ADD REPLYlink written 3 months ago by James W. MacDonald45k
1

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; message No 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?

 

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite("pd.hg.u133.plus.2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.1 (2017-06-30).
Installing package(s) ‘pd.hg.u133.plus.2’
installing the source package ‘pd.hg.u133.plus.2’

trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/pd.hg.u133.plus.2_3.12.0.tar.gz'
Content type 'application/x-gzip' length 24799467 bytes (23.7 MB)
downloaded 23.7 MB

* installing *source* package 'pd.hg.u133.plus.2' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
No methods found in "RSQLite" for requests: dbGetQuery
*** arch - x64
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (pd.hg.u133.plus.2)

The downloaded source packages are in
        ‘D:\TMP\Rtmpe8reJv\downloaded_packages’
> sessionInfo()
R version 3.4.1 (2017-06-30)
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_3.4.1 tools_3.4.1   
>

 

ADD REPLYlink written 3 months ago by Guido Hooiveld2.2k

<<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 (though No methods message is returned).

ADD REPLYlink modified 3 months ago • written 3 months ago by Guido Hooiveld2.2k

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.

ADD REPLYlink written 3 months ago by James W. MacDonald45k
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