Dear Martin, Thank you for the quick response - you are right to suspect bowtie, it seems that version 1.1.1 which I am using in Rbowtie has an issue on newer macOS versions, and I am currently looking into wether an update to version 1.2 would fix this.
A first issue that I stumbled into is that R CMD check now warns about the bowtie code using C++11 extensions. Following the manual, I have added the following to DESCRIPTION: SystemRequirements: GNU make, C++11 ("GNU make" was already there), but the field seems to be ignored by R CMD check and the warning persists. Is this something to worry about? I hope to get back with a solution for the bowtie issue soon. 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@BABCBBBABABA?A>8>A7:6=@>>:@BAA>1;B\tXM:i:0" > > [2] > "seq10138\t4\t*\t0\t0\t*\t*\t0\t0\tCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTC\tABBBBBBBBBBBBBBB@CBBBA9BB@>'>9@AA=A?\tXM:i:0" > > [3] > "seq10139\t4\t*\t0\t0\t*\t*\t0\t0\tCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAAT\tBBCBBCBBBBBBBB=ABBBB@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@AAB@BBBA@B@ABAABBABAA@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.mor...@roswellpark.org] >>>>> Sent: Tuesday, 11 April 2017 7:20 PM >>>>> To: Gordon K Smyth <sm...@wehi.edu.au>; bioc-devel@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@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@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. 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