[Bioc-devel] Using BiocInstaller with R 3.4.0 beta

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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