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" <lg...@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 <dtene...@fredhutch.org> >>> wrote: >>> >>>> >>>> >>>> ----- Original Message ----- >>>> > From: "Laurent Gatto" <lg...@cam.ac.uk> >>>> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> >>>> > Cc: "Martin Morgan" <mtmor...@fredhutch.org>, >>>>bioc-devel@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" <mtmor...@fredhutch.org> >>>> > >> To: "Laurent Gatto" <lg...@cam.ac.uk>, bioc-devel@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@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@r-project.org mailing list >>>> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> > >> >>>> > >>>> > -- >>>> > Laurent Gatto >>>> > http://cpu.sysbiol.cam.ac.uk/ >>>> > >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> >> >>-- >>Laurent Gatto >>http://cpu.sysbiol.cam.ac.uk/ >> >>_______________________________________________ >>Bioc-devel@r-project.org mailing list >>https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Laurent Gatto http://cpu.sysbiol.cam.ac.uk/ _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel