[Bioc-devel] error: 2 arguments passed to .Internal(ls) which requires 3

Hahne, Florian florian.hahne at novartis.com
Wed Nov 5 09:19:43 CET 2014 

Hi Laurent,
I had a similar issue a couple of days ago, but the error would only show
up when building the vignette of a package, rather than during package
loading. I tried to dig around for a while but really could not find the
bottom of this. In the end I decided to update my R-devel version, and
reinstall all packages with
biocLite(rownames(installed.packages()))
This fixed the problem in the end. A bit of a blunt tool, I agree, but in
the end probably faster than hours of debugging the package load chain...
Hope that helps,
Florian

On 05/11/14 01:55, "Laurent Gatto" <lg390 at cam.ac.uk> wrote:

>
>On  4 November 2014 20:27, Kasper Daniel Hansen wrote:
>
>> Laurent,
>>
>> If you do
>>   installed.packages()
>> (note the 'ed') you are told which version of R was used to build the
>> package.  This has sometimes been useful to me in these kind of
>>situations.
>
>Just to follow up, I got rid of all packages that were built using R <
>3.2.0, but no luck:
>
>> ip <- installed.packages()
>> table(ip[, "Built"])
>3.2.0 
>  911 
>> library("BiocInstaller")
>Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help
>> biocLite("Homo.sapiens")
>BioC_mirror: http://bioconductor.org
>Using Bioconductor version 3.1 (BiocInstaller 1.17.1), R version 3.2.0.
>Installing package(s) 'Homo.sapiens'
>trying URL 
>'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/Homo.sap
>iens_1.1.2.tar.gz'
>Content type 'application/x-gzip' length 1511 bytes
>opened URL
>==================================================
>downloaded 1511 bytes
>
>* installing *source* package ŒHomo.sapiens¹ ...
>** R
>** data
>** preparing package for lazy loading
>Error : .onLoad failed in loadNamespace() for 'GO.db', details:
>  call: ls(envir, all.names = TRUE)
>  error: 2 arguments passed to .Internal(ls) which requires 3
>Error : package ŒGO.db¹ could not be loaded
>ERROR: lazy loading failed for package ŒHomo.sapiens¹
>* removing 
>Œ/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2/Homo.sapiens¹
>
>Same also with ChIPpeakAnno/GO.db now.
>
>Will investigate further tomorrow.
>
>Laurent
>
>> Best,
>> Kasper
>>
>> On Tue, Nov 4, 2014 at 2:18 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
>> wrote:
>>
>>>
>>>
>>> ----- Original Message -----
>>> > From: "Laurent Gatto" <lg390 at cam.ac.uk>
>>> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
>>> > Cc: "Martin Morgan" <mtmorgan at fredhutch.org>,
>>>bioc-devel at r-project.org
>>> > Sent: Tuesday, November 4, 2014 11:14:08 AM
>>> > Subject: Re: [Bioc-devel] error: 2 arguments passed to .Internal(ls)
>>> which requires 3
>>> >
>>> >
>>> > On  4 November 2014 15:55, Dan Tenenbaum wrote:
>>> >
>>> > > Hi Laurent,
>>> > >
>>> > > ----- Original Message -----
>>> > >> From: "Martin Morgan" <mtmorgan at fredhutch.org>
>>> > >> To: "Laurent Gatto" <lg390 at cam.ac.uk>, bioc-devel at r-project.org
>>> > >> Sent: Tuesday, November 4, 2014 5:41:04 AM
>>> > >> Subject: Re: [Bioc-devel] error: 2 arguments passed to
>>> > >> .Internal(ls) which requires 3
>>> > >>
>>> > >> Hi Laurent --
>>> > >>
>>> > >> On 11/04/2014 01:33 AM, Laurent Gatto wrote:
>>> > >> >
>>> > >> > Something's fishy with my R devel/Bioc 3.1 installation and I
>>> > >> > fail
>>> > >> > to
>>> > >> > see what is wrong.
>>> > >> >
>>> > >> > I want to install Homo.sapiens:
>>> > >> >
>>> > >> >> library("BiocInstaller")
>>> > >> > ## Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite
>>> > >> > for
>>> > >> > help
>>> > >> >> biocLite("Homo.sapiens")
>>> > >> > ## BioC_mirror: http://bioconductor.org
>>> > >> > ## Using Bioconductor version 3.1 (BiocInstaller 1.17.1), R
>>> > >> > version
>>> > >> > 3.2.0.
>>> > >> > ## Installing package(s) 'Homo.sapiens'
>>> > >> > ## trying URL
>>> > >> > '
>>> 
>>>http://bioconductor.org/packages/3.1/data/annotation/src/contrib/Homo.sa
>>>piens_1.1.2.tar.gz
>>> '
>>> > >> > ## Content type 'application/x-gzip' length 1511 bytes
>>> > >> > ## opened URL
>>> > >> > ## ==================================================
>>> > >> > ## downloaded 1511 bytes
>>> > >> > ##
>>> > >> > ## * installing *source* package ŒHomo.sapiens¹ ...
>>> > >> > ## ** R
>>> > >> > ## ** data
>>> > >> > ## ** preparing package for lazy loading
>>> > >> > ## Error : .onLoad failed in loadNamespace() for 'GO.db',
>>> > >> > details:
>>> > >> > ##   call: ls(envir, all.names = TRUE)
>>> > >> > ##   error: 2 arguments passed to .Internal(ls) which requires 3
>>> > >> > ## Error : package ŒGO.db¹ could not be loaded
>>> > >> > ## ERROR: lazy loading failed for package ŒHomo.sapiens¹
>>> > >> > ## * removing
>>> > >> > 
>>>Œ/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2/Homo.sapiens¹
>>> > >> > ## * restoring previous
>>> > >> > 
>>>Œ/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2/Homo.sapiens¹
>>> > >> > ##
>>> > >> > ## The downloaded source packages are in
>>> > >> > ##       Œ/tmp/RtmpXYXfis/downloaded_packages¹
>>> > >> > ## Warning message:
>>> > >> > ## In install.packages(pkgs = pkgs, lib = lib, repos = repos,
>>> > >> > ...)
>>> > >> > :
>>> > >> > ##   installation of package ŒHomo.sapiens¹ had non-zero exit
>>> > >> > status
>>> > >> >
>>> > >> > GO.db is up-to-date, but let's (successfully) biocLite and load
>>> > >> > it:
>>> > >> >
>>> > >> >> biocLite("GO.db")
>>> > >> > ## BioC_mirror: http://bioconductor.org
>>> > >> > ## Using Bioconductor version 3.1 (BiocInstaller 1.17.1), R
>>> > >> > version
>>> > >> > 3.2.0.
>>> > >> > ## Installing package(s) 'GO.db'
>>> > >> > ## trying URL
>>> > >> > '
>>> 
>>>http://bioconductor.org/packages/3.1/data/annotation/src/contrib/GO.db_3
>>>.0.0.tar.gz
>>> '
>>> > >> > ## Content type 'application/x-gzip' length 28747892 bytes (27.4
>>> > >> > MB)
>>> > >> > ## opened URL
>>> > >> > ## ==================================================
>>> > >> > ## downloaded 27.4 MB
>>> > >> > ##
>>> > >> > ## * installing *source* package ŒGO.db¹ ...
>>> > >> > ## ** R
>>> > >> > ## ** inst
>>> > >> > ## ** preparing package for lazy loading
>>> > >> > ## ** help
>>> > >> > ## *** installing help indices
>>> > >> > ## ** building package indices
>>> > >> > ## ** testing if installed package can be loaded
>>> > >> > ## * DONE (GO.db)
>>> > >> > ##
>>> > >> > ## The downloaded source packages are in
>>> > >> > ##       Œ/tmp/Rtmprr15y4/downloaded_packages¹
>>> > >> >> suppressPackageStartupMessages(library("GO.db"))
>>> > >> >
>>> > >> > Repeating unsuccessful attempt to install Homo.sapiens fails
>>> > >> > again:
>>> > >> >
>>> > >> >> bioclite("homo.sapiens")
>>> > >> > ## bioc_mirror: http://bioconductor.org
>>> > >> > ## using bioconductor version 3.1 (biocinstaller 1.17.1), r
>>> > >> > version
>>> > >> > 3.2.0.
>>> > >> > ## installing package(s) 'homo.sapiens'
>>> > >> > ## trying url
>>> > >> > '
>>> 
>>>http://bioconductor.org/packages/3.1/data/annotation/src/contrib/homo.sa
>>>piens_1.1.2.tar.gz
>>> '
>>> > >> > ## content type 'application/x-gzip' length 1511 bytes
>>> > >> > ## opened url
>>> > >> > ## ==================================================
>>> > >> > ## downloaded 1511 bytes
>>> > >> > ##
>>> > >> > ## * installing *source* package Œhomo.sapiens¹ ...
>>> > >> > ## ** r
>>> > >> > ## ** data
>>> > >> > ## ** preparing package for lazy loading
>>> > >> > ## error : .onload failed in loadnamespace() for 'go.db',
>>> > >> > details:
>>> > >> > ##   call: ls(envir, all.names = true)
>>> > >> > ##   error: 2 arguments passed to .internal(ls) which requires 3
>>> > >> > ## error : package Œgo.db¹ could not be loaded
>>> > >> > ## error: lazy loading failed for package Œhomo.sapiens¹
>>> > >> > ## * removing
>>> > >> > 
>>>Œ/home/lg390/r/x86_64-unknown-linux-gnu-library/3.2/homo.sapiens¹
>>> > >> > ## * restoring previous
>>> > >> > 
>>>Œ/home/lg390/r/x86_64-unknown-linux-gnu-library/3.2/homo.sapiens¹
>>> > >> > ##
>>> > >> > ## the downloaded source packages are in
>>> > >> > ##       Œ/tmp/rtmprr15y4/downloaded_packages¹
>>> > >> > ## warning message:
>>> > >> > ## in install.packages(pkgs = pkgs, lib = lib, repos = repos,
>>> > >> > ...)
>>> > >> > :
>>> > >> > ##   installation of package Œhomo.sapiens¹ had non-zero exit
>>> > >> > status
>>> > >> >
>>> > >> > I have the exact same error with ReportingTools/PFAM.db,
>>> > >> > Mus.musculus/GO.db and probably others.
>>> > >> >
>>> > >> > Session info with other relevant package versions below. I
>>> > >> > experienced
>>> > >> > the same error with a slightly older R-devel (2014-10-29
>>> > >> > r66897).
>>> > >> >
>>> > >> > Any hints?
>>> > >>
>>> > >> Somewhere I think there's a stale serialized R-3.1 reference to
>>> > >> ls(),
>>> > >> derived
>>> > >> from a package build with R-3.1 rather than R-devel.
>>> > >>
>>> > >> A little detective work shows that packages are loaded in the
>>> > >> following order
>>> > >>
>>> > >> ...
>>> > >> [43] "graph"                             "RBGL"
>>> > >> [45] "GO.db"                             "org.Hs.eg.db"
>>> > >> [47] "TxDb.Hsapiens.UCSC.hg19.knownGene" "Homo.sapiens"
>>> > >>
>>> > >> so I wonder if org.Hs.eg.db or TxDb.... is actually the problem,
>>> > >> and
>>> > >> biocLite(org.Hs.eg.db) or TxDb... (maybe with type="source") would
>>> > >> help?
>>> > >>
>>> > >> It might help to (maybe before biocLite(), to find the source of
>>> > >> the
>>> > >> problem)
>>> > >>
>>> > >> biocLite("Homo.sapiens", INSTALL_opts="--no-test-load")
>>> > >>
>>> > >> and then
>>> > >>
>>> > >>    library(Homo.sapiens)
>>> > >>
>>> > >> followed by traceback() -- this way you'll at least be able to
>>> > >> explore the call
>>> > >> stack.
>>> > >>
>>> > >
>>> > >
>>> > > Didn't you report this same problem the other day and the solution
>>> > > was
>>> > > to update all your packages?
>>> >
>>> > Yes, and that was Go.db that failed. Updating to AnnotationDbi 1.29.1
>>> > fixed it.
>>> >
>>> > > Note that both installed.packages() and packageDescription()
>>> > > display
>>> > > information about the version of R under which a given package was
>>> > > built.
>>> > > So that could help narrow things down. It's almost certainly an
>>> > > annotation package, because almost all of the ones in our devel
>>> > > repository are just copied from our release repository and built
>>> > > under
>>> > > R-3.1.x. So we might need to rebuild them under R-devel, at least
>>> > > the
>>> > > ones with stale serialized references.
>>> >
>>> > Ok, I guess I will go ahead and hunt all annotation packages.
>>> >
>>> > What is the best way to programmatically get a list of all annotation
>>> > packages - biocViews? While thinking about a question that came up on
>>> > the support site, I realised that I did not even know if the
>>> > annotation
>>> > packages lived in an svn repo.
>>> >
>>>
>>> Actually, the fact that an AnnotationDbi update fixed your earlier
>>>issue
>>> makes me unsure about whether the "bad" package you have is an
>>>annotation
>>> package.
>>>
>>> But if you still want to know....You can look at
>>> 
>>>http://bioconductor.org/packages/devel/data/annotation/src/contrib/PACKA
>>>GES
>>> or available.packages() which tells you what repository a package comes
>>> from.
>>>
>>> Dan
>>>
>>>
>>> > Laurent
>>> >
>>> > > Dan
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >> Martin
>>> > >>
>>> > >>
>>> > >> >
>>> > >> > Best wishes,
>>> > >> >
>>> > >> > Laurent
>>> > >> >
>>> > >> >> library("RSQLite")
>>> > >> >> library("AnnotationDbi")
>>> > >> >> sessionInfo()
>>> > >> > ## R Under development (unstable) (2014-11-01 r66923)
>>> > >> > ## Platform: x86_64-unknown-linux-gnu (64-bit)
>>> > >> > ##
>>> > >> > ## locale:
>>> > >> > ##  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>>> > >> > ##  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>>> > >> > ##  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>>> > >> > ##  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>>> > >> > ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> > >> > ## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>> > >> > ##
>>> > >> > ## attached base packages:
>>> > >> > ## [1] parallel  stats4    stats     graphics  grDevices utils
>>> > >> >     datasets
>>> > >> > ## [8] methods   base
>>> > >> > ##
>>> > >> > ## other attached packages:
>>> > >> > ##  [1] GO.db_3.0.0          RSQLite_1.0.0        DBI_0.3.1
>>> > >> > ##  [4] AnnotationDbi_1.29.1 GenomeInfoDb_1.3.6   IRanges_2.1.4
>>> > >> > ##  [7] S4Vectors_0.5.2      Biobase_2.27.0
>>> > >> >       BiocGenerics_0.13.0
>>> > >> > ## [10] BiocInstaller_1.17.1
>>> > >> > ##
>>> > >> > ## loaded via a namespace (and not attached):
>>> > >> > ## [1] compiler_3.2.0 tools_3.2.0
>>> > >> >
>>> > >> > _______________________________________________
>>> > >> > Bioc-devel at r-project.org mailing list
>>> > >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> > >> >
>>> > >>
>>> > >>
>>> > >> --
>>> > >> Computational Biology / Fred Hutchinson Cancer Research Center
>>> > >> 1100 Fairview Ave. N.
>>> > >> PO Box 19024 Seattle, WA 98109
>>> > >>
>>> > >> Location: Arnold Building M1 B861
>>> > >> Phone: (206) 667-2793
>>> > >>
>>> > >> _______________________________________________
>>> > >> Bioc-devel at r-project.org mailing list
>>> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> > >>
>>> >
>>> > --
>>> > Laurent Gatto
>>> > http://cpu.sysbiol.cam.ac.uk/
>>> >
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>
>-- 
>Laurent Gatto
>http://cpu.sysbiol.cam.ac.uk/
>
>_______________________________________________
>Bioc-devel at r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/bioc-devel

More information about the Bioc-devel mailing list