[Bioc-devel] Using BiocInstaller with R 3.4.0 beta
Michael Stadler
michael.stadler at fmi.ch
Wed Apr 19 11:45:34 CEST 2017
Dear BioC core,
Thanks for the report, Herve. If I understand correctly, there is
nothing I can do at this point to make QuasR green on windows, correct?
I have another question regarding QuasR not building on veracruz2: The
vignette does not build currently, reporting:
Error on veracruz2.bioconductor.org processing sample
/tmp/RtmpJBWrjI/chip_1_1.fq.bz2df0b6901ff33.fastq : 'asBam' internal:
samtools invoked 'abort' ...
Though it seems to build fine on other platforms, and there were no
recent changes to the vignette. What would you or other suggest to do
about that?
Any suggestions are appreciated,
Michael
On 17.04.2017 02:08, Hervé Pagès wrote:
> FWIW here are all the packages that are victim of this
> installed.packages bug in today's build report:
>
> alpine
> fCI
> GenomicFeatures
> QuasR
>
> We only see this error on tokay2 (Windows).
>
> H.
>
>
> On 04/11/2017 04:21 PM, Gordon K Smyth wrote:
>> I restarted my PC this morning and the problem disappeared.
>>
>> I probably should have tried that last night, but it was late ...
>>
>> Thanks
>> Gordon
>>
>>> -----Original Message-----
>>> From: Martin Morgan [mailto:martin.morgan at roswellpark.org]
>>> Sent: Tuesday, 11 April 2017 7:20 PM
>>> To: Gordon K Smyth <smyth at wehi.edu.au>; bioc-devel at r-project.org
>>> Subject: Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta
>>>
>>> On 04/11/2017 05:01 AM, Gordon K Smyth wrote:
>>>> The problem appears to be with installed.packages(). If I start a
>>>> fresh R
>>> 3.4.0beta session, then I can run installed.packages() once with
>>> correct results,
>>> but running it a second time gives the error message:
>>>>
>>>>> installed.packages()
>>>> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib)
>>>> && :
>>>> missing value where TRUE/FALSE needed
>>>
>>> The test is in this code chunk, from utils/R/packages.R
>>>
>>> for(lib in lib.loc) {
>>> if(noCache) {
>>> ret0 <- .readPkgDesc(lib, fields)
>>> if(length(ret0)) retval <- rbind(retval, ret0)
>>> } else {
>>> ## Previously used URLencode for e.g. Windows paths with
>>> drives
>>> ## This version works for very long file names.
>>> base <- paste(c(lib, fields), collapse = ",")
>>> ## add length and 64-bit CRC in hex (in theory, seems
>>> ## it is actually 32-bit on some systems)
>>> enc <- sprintf("%d_%s", nchar(base), .Call(C_crc64, base))
>>> dest <- file.path(tempdir(), paste0("libloc_", enc,
>>> ".rds"))
>>> if(file.exists(dest) &&
>>> file.mtime(dest) > file.mtime(lib) &&
>>> (val <- readRDS(dest))$base == base)
>>> ## use the cache file
>>> retval <- rbind(retval, val$value)
>>> else {
>>> ret0 <- .readPkgDesc(lib, fields)
>>> if(length(ret0)) {
>>> retval <- rbind(retval, ret0)
>>> ## save the cache file
>>> saveRDS(list(base = base, value = ret0), dest)
>>> }
>>> }
>>> }
>>>
>>>
>>> where 'lib' is one of .libPaths(), 'dest' is one of
>>>
>>> dir(tempdir(), pattern="libloc_", full=TRUE)
>>>
>>> and 'base' should be a character(1)
>>>
>>> I think the code chunk has tried to cache the packages installed in each
>>> directory of .libPaths() (the saveRDS() line), and these are somehow
>>> corrupted on the second time through (I guess evaluating the
>>> readRDS()??).
>>>
>>> For instance I have two paths in .libPaths() and after the first
>>> install.packages() I have
>>>
>>> > str(readRDS(dir(tempdir(), full=TRUE)[1]))
>>> List of 2
>>> $ base : chr
>>> "/home/mtmorgan/bin/R-3-4-
>>> branch/library,Version,Priority,Depends,Imports,LinkingTo,Suggests,Enhances,Li
>>>
>>> cense,Li"|
>>> __truncated__
>>> $ value: chr [1:29, 1:17] "base" "boot" "class" "cluster" ...
>>> > str(readRDS(dir(tempdir(), full=TRUE)[2]))
>>> List of 2
>>> $ base : chr
>>> "/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.4-Bioc-
>>> 3.5,Version,Priority,Depends,Imports,LinkingTo,Suggests,E"|
>>> __truncated__
>>> $ value: chr [1:513, 1:17] "abind" "acepack" "aCGH" "ADaCGH2" ...
>>>
>>> I'm guessing that one of these files is corrupted somehow, but it's not
>>> obvious how. Can you use options(error=recover) and find the values that
>>> cause the conditional to fail?
>>>
>>> Martin
>>>
>>>>
>>>>
>>>>> -----Original Message-----
>>>>> From: Gordon K Smyth
>>>>> Sent: Tuesday, 11 April 2017 6:26 PM
>>>>> To: bioc-devel at r-project.org
>>>>> Subject: Using BiocInstaller with R 3.4.0 beta
>>>>>
>>>>> I thought I would test out R 3.4.0 beta (for Windows) but now I
>>>>> can't use the
>>>>> BiocInstaller package. Attempts to use biocLite() or biocValid()
>>>>> lead to an
>>> error
>>>>> message as shown below.
>>>>>
>>>>> What have I overlooked?
>>>>>
>>>>> Thanks
>>>>> Gordon
>>>>>
>>>>>> sessionInfo()
>>>>> R version 3.4.0 beta (2017-04-08 r72499)
>>>>> 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_Australia.1252 LC_CTYPE=English_Australia.1252
>>>>> LC_MONETARY=English_Australia.1252
>>>>> [4] LC_NUMERIC=C LC_TIME=English_Australia.1252
>>>>>
>>>>> attached base packages:
>>>>> [1] stats graphics grDevices utils datasets methods base
>>>>>
>>>>> loaded via a namespace (and not attached):
>>>>> [1] compiler_3.4.0
>>>>>> remove.packages("BiocInstaller")
>>>>> Removing package from 'C:/lib/R/R-3.4.0beta/library'
>>>>> (as 'lib' is unspecified)
>>>>> Error in find.package(pkgs, lib) :
>>>>> there is no package called 'BiocInstaller'
>>>>>> source("https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_biocLite.R&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qQj20RkrlTIRAItC1ZQMStpDs5hOqJaHLGXLTycSugE&s=6ODigHgwIN79ejt5MJf2kpj1UREzVRkiKBpOWsY_J-I&e=
>>>>>> ")
>>>>> trying URL
>>>>>
>>> 'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.5_bioc_bin_windows_contrib_3.4_BiocInst&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qQj20RkrlTIRAItC1ZQMStpDs5hOqJaHLGXLTycSugE&s=n0cklbnoQ9a2xy8zQvs0mMdS3tP5gk2NbVWsALYoXOk&e=
>>>
>>>>> aller_1.25.3.zip'
>>>>> Content type 'application/zip' length 127489 bytes (124 KB)
>>>>> downloaded 124 KB
>>>>>
>>>>> package 'BiocInstaller' successfully unpacked and MD5 sums checked
>>>>>
>>>>> The downloaded binary packages are in
>>>>>
>>>>> C:\Users\smyth\AppData\Local\Temp\RtmpOUhCbB\downloaded_packages
>>>>> Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
>>>>>> BiocInstaller::biocValid()
>>>>> Error in if (file.exists(dest) && file.mtime(dest) >
>>>>> file.mtime(lib) && :
>>>>> missing value where TRUE/FALSE needed
>>>>>
>>>>>
>>>>> ---------------------------------------------
>>>>> Professor Gordon K Smyth,
>>>>> Head, Bioinformatics Division,
>>>>> Walter and Eliza Hall Institute of Medical Research,
>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.statsci.org_smyth&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qQj20RkrlTIRAItC1ZQMStpDs5hOqJaHLGXLTycSugE&s=N8BZ6_dazp5kboftdMZCE4ip8G9ORI9zTd8TVRI4eB0&e=
>>>>>
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qQj20RkrlTIRAItC1ZQMStpDs5hOqJaHLGXLTycSugE&s=f74EDfuo7C_LCPCfcGAREY8dqBJwwjc5DqM7YF7Tvg4&e=
>>>>
>>>>
>>>
>>>
>>> This email message may contain legally privileged and/or confidential
>>> information. If you are not the intended recipient(s), or the
>>> employee or agent
>>> responsible for the delivery of this message to the intended
>>> recipient(s), you are
>>> hereby notified that any disclosure, copying, distribution, or use of
>>> this email
>>> message is prohibited. If you have received this message in error,
>>> please notify
>>> the sender immediately by e-mail and delete this email message from your
>>> computer. Thank you.
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qQj20RkrlTIRAItC1ZQMStpDs5hOqJaHLGXLTycSugE&s=f74EDfuo7C_LCPCfcGAREY8dqBJwwjc5DqM7YF7Tvg4&e=
>>
>>
>
More information about the Bioc-devel
mailing list