[Bioc-devel] Using BiocInstaller with R 3.4.0 beta
Hervé Pagès
hpages at fredhutch.org
Thu Apr 20 02:08:14 CEST 2017
On 04/19/2017 02:45 AM, Michael Stadler wrote:
> 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?
Nothing you can do in QuasR itself. Sorry that I don't have time to do
this but someone would need to take a close look at this problem though.
And report his/her findings to the R folks. We're running short of time!
(will be a bummer to have R 3.4 released with such a nasty bug in it)
Cheers,
H.
>
> 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=
>>>
>>>
>>
>
> _______________________________________________
> 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=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-B0JUY5jly6i3m8Z4wuHZJVQt5ycjvrycyhxwpwrUfU&s=WPdjIQrswV-5SNRD7DpJ_Gy8IWDrNlyxmE8lilh6azA&e=
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
More information about the Bioc-devel
mailing list