[Bioc-devel] Using BiocInstaller with R 3.4.0 beta
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, Herv? Pag?s 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=
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