[Bioc-devel] Using BiocInstaller with R 3.4.0 beta
Michael Stadler
michael.stadler at fmi.ch
Thu Apr 20 09:08:14 CEST 2017
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.
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
>>>>>> 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=
>>>>>>
>>>>>>
>>>>>>
>>>>>
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>>>>
>>>>
>>>>
>>>
>>
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