[Bioc-devel] Using BiocInstaller with R 3.4.0 beta
Martin Morgan
martin.morgan at roswellpark.org
Thu Apr 20 11:09:30 CEST 2017
On 04/20/2017 03:08 AM, Michael Stadler wrote:
> Dear Martin,
>
> I've now spend a day trying to resolve this. To make a long story short:
> I could get bowtie 1.1.1 (currently used in Rbowtie 1.15.1) to compile
> and work under macOS Sierra.
>
> I tried updating bowtie, but:
> - bowtie 1.2 has a bug that prevents it from using multiple threads,
> which I could reproduce both under Linux and macOS Sierra and which I
> could not resolve (see https://github.com/BenLangmead/bowtie/issues/41).
> - bowtie 1.1.2 crashes if compiled with clang (see
> https://github.com/BenLangmead/bowtie/issues/21), the only known
> workaround being to use a different toolchain, which I think is not an
> option for BioC/Rbowtie.
>
> I hope that resolves also the issue on El Capitan.
Thanks, it seems like the best available solution. Martin
>
> Michael
>
> On 19.04.2017 13:47, Martin Morgan wrote:
>> On 04/19/2017 05:45 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?
>>>
>>> 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?
>>
>> The error is in createGenomicAlignmentsController after
>>
>> https://github.com/Bioconductor-mirror/QuasR/blob/cc374678033055f2bd4d105c502a426807223c1c/R/createAlignments-functions.R#L292
>>
>>
>> it looks like the sam file is quite funky
>>
>> Browse[4]> options(nwarnings=10000)
>> Browse[4]> xx = readLines(samFile)
>> There were 2339 warnings (use warnings() to see them)
>> Browse[4]> head(warnings(), 3)
>> Warning messages:
>> 1: In readLines(samFile) : line 7 appears to contain an embedded nul
>> 2: In readLines(samFile) : line 8 appears to contain an embedded nul
>> 3: In readLines(samFile) : line 9 appears to contain an embedded nul
>> Browse[4]> table(nzchar(xx))
>>
>> FALSE TRUE
>> 2341 261
>> Browse[4]> substring(head(xx, 10), 1, 70)
>> [1] "@HD\tVN:1.0\tSO:unsorted"
>> [2] "@SQ\tSN:chr1\tLN:40000"
>> [3] "@SQ\tSN:chr2\tLN:10000"
>> [4] "@SQ\tSN:chr3\tLN:45000"
>> [5]
>> "@PG\tID:Bowtie\tVN:1.1.1\tCL:\"/Library/Frameworks/R.framework/Versions/3."
>>
>> [6] ""
>> [7] ""
>> [8] ""
>> [9] ""
>> [10] ""
>>
>> The 'abort' from Rsamtools is
>>
>> Parse error at line 143: missing colon in auxiliary data
>>
>> It's not really clear whether R is being confused by the embedded nulls
>> or blank lines or other problem
>>
>> Browse[4]> xx[140 + 1:5]
>> [1] "" "" "" "" ""
>> Browse[4]> xx[nzhchar(xx)][140 + 1:5]
>> Error in nzhchar(xx) : could not find function "nzhchar"
>> Browse[4]> xx[nzchar(xx)][140 + 1:5]
>> [1]
>> "seq10137\t4\t*\t0\t0\t*\t*\t0\t0\tTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACAT\tB at BABCBBBABABA?A>8>A7:6=@>>:@BAA>1;B\tXM:i:0"
>>
>> [2]
>> "seq10138\t4\t*\t0\t0\t*\t*\t0\t0\tCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTC\tABBBBBBBBBBBBBBB at CBBBA9BB@>'>9 at AA=A?\tXM:i:0"
>>
>> [3]
>> "seq10139\t4\t*\t0\t0\t*\t*\t0\t0\tCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAAT\tBBCBBCBBBBBBBB=ABBBB at BAABBABBA=A??><\tXM:i:0"
>>
>> [4]
>> "seq10140\t4\t*\t0\t0\t*\t*\t0\t0\tGGTTGTCAGCGTCATAAGAGGTTTTACCTCCAAATG\t;;;AA=AA<AA<ABBB?=@>>=CCBB>9@@>B=BB=\tXM:i:0"
>>
>> [5]
>> "seq10141\t4\t*\t0\t0\t*\t*\t0\t0\tAACCCTAATGAGCTTAATCAAGATGATGCTCGTTAT\tBBABBBBB at AAB@BBBA at B@ABAABBABAA at B?A?@\tXM:i:0"
>>
>>
>> So I guess it's in creation of the sam file -- Bowtie?
>>
>> Martin
>>
>>>
>>> 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
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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
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>>>>>
>>>>>
>>>>
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