EatonEtAlChIPseq 0.9.0
Patrick Aboyoun
| Snapshot Date: 2015-10-24 10:15:05 -0400 (Sat, 24 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/EatonEtAlChIPseq | | Last Changed Rev: 3462 / Revision: 3473 | | Last Changed Date: 2015-10-13 16:20:35 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | | |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK | |
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###
### Running command:
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### rm -rf EatonEtAlChIPseq.buildbin-libdir EatonEtAlChIPseq.Rcheck && mkdir EatonEtAlChIPseq.buildbin-libdir EatonEtAlChIPseq.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EatonEtAlChIPseq.buildbin-libdir EatonEtAlChIPseq_0.9.0.tar.gz >EatonEtAlChIPseq.Rcheck\00install.out 2>&1 && cp EatonEtAlChIPseq.Rcheck\00install.out EatonEtAlChIPseq-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=EatonEtAlChIPseq.buildbin-libdir --install="check:EatonEtAlChIPseq-install.out" --force-multiarch --no-vignettes --timings EatonEtAlChIPseq_0.9.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-data-experiment/meat/EatonEtAlChIPseq.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EatonEtAlChIPseq/DESCRIPTION' ... OK
* this is package 'EatonEtAlChIPseq' version '0.9.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'EatonEtAlChIPseq' can be installed ... OK
* checking installed package size ... NOTE
installed size is 20.6Mb
sub-directories of 1Mb or more:
extdata 20.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
Artistic 2.0
Standardizable: TRUE
Standardized license specification:
Artistic-2.0
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
Error: Input/Output
'readAligned' failed to parse files
dirPath: 'c:/biocbld/bbs-3.3-data-experiment/meat/EatonEtAlChIPseq.buildbin-libdir/EatonEtAlChIPseq/extdata/GSM424494_wt_G2_orc_chip_rep1_S288C_14.mapview.txt.gz'
pattern: ''
type: 'MAQMapview'
error: invalid class "IntegerQuality" object: invalid object for slot "quality" in class "IntegerQuality": got class "character", should be or extend class "integer"
Call sequence:
13: .throw(SRError("Input/Output", msg))
12: .throw(SRError("Input/Output", msg))
11: value[[3L]](cond)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch({
switch(type, SolexaExport = .readAligned_SolexaExport(dirPath,
pattern = pattern, ...), SolexaPrealign = , SolexaAlign = ,
SolexaRealign = .readAligned_SolexaAlign(dirPath, pattern = pattern,
...), SolexaResult = .readAligned_SolexaResult(dirPath,
pattern = pattern, ..
Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'EatonEtAlChIPseq-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: orcAligns
> ### Title: Alignments of ChIP-seq data to yeast chromosome XIV
> ### Aliases: orcAlignsRep1 orcAlignsRep2
> ### Keywords: datasets
>
> ### ** Examples
>
> data(orcAlignsRep1)
Warning in read.table(file = file, header = header, sep = sep, quote = quote, :
not all columns named in 'colClasses' exist
Error: Input/Output
'readAligned' failed to parse files
dirPath: 'c:/biocbld/bbs-3.3-data-experiment/meat/EatonEtAlChIPseq.buildbin-libdir/EatonEtAlChIPseq/extdata/GSM424494_wt_G2_orc_chip_rep1_S288C_14.mapview.txt.gz'
pattern: ''
type: 'MAQMapview'
error: invalid class "IntegerQuality" object: invalid object for slot "quality" in class "IntegerQuality": got class "character", should be or extend class "integer"
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'EatonEtAlChIPseq-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: orcAligns
> ### Title: Alignments of ChIP-seq data to yeast chromosome XIV
> ### Aliases: orcAlignsRep1 orcAlignsRep2
> ### Keywords: datasets
>
> ### ** Examples
>
> data(orcAlignsRep1)
Warning in read.table(file = file, header = header, sep = sep, quote = quote, :
not all columns named in 'colClasses' exist
Error: Input/Output
'readAligned' failed to parse files
dirPath: 'c:/biocbld/bbs-3.3-data-experiment/meat/EatonEtAlChIPseq.buildbin-libdir/EatonEtAlChIPseq/extdata/GSM424494_wt_G2_orc_chip_rep1_S288C_14.mapview.txt.gz'
pattern: ''
type: 'MAQMapview'
error: invalid class "IntegerQuality" object: invalid object for slot "quality" in class "IntegerQuality": got class "character", should be or extend class "integer"
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 3 NOTEs
See
'c:/biocbld/bbs-3.3-data-experiment/meat/EatonEtAlChIPseq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'EatonEtAlChIPseq' ...
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
install for x64
* installing *source* package 'EatonEtAlChIPseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EatonEtAlChIPseq' as EatonEtAlChIPseq_0.9.0.zip
* DONE (EatonEtAlChIPseq)