[Bioc-devel] error: 2 arguments passed to .Internal(ls) which requires 3
Laurent Gatto
lg390 at cam.ac.uk
Wed Nov 5 10:35:39 CET 2014
On 5 November 2014 08:19, Hahne, Florian wrote:
> 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...
Thanks, Florian. I think I will follow you suggestion.
Best wishes,
Laurent
> 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
--
Laurent Gatto
http://cpu.sysbiol.cam.ac.uk/
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