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BioC experimental data: CHECK report for RNAseqData.HeLa.bam.chr14 on moscato2

This page was generated on 2014-01-06 16:08:00 -0800 (Mon, 06 Jan 2014).

Package 156/186HostnameOS / ArchBUILDCHECKBUILD BIN
RNAseqData.HeLa.bam.chr14 0.1.6
H. Pages
Snapshot Date: 2014-01-06 07:15:21 -0800 (Mon, 06 Jan 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RNAseqData.HeLa.bam.chr14
Last Changed Rev: 2646 / Revision: 2662
Last Changed Date: 2013-12-13 11:44:17 -0800 (Fri, 13 Dec 2013)
zin2 Linux (Ubuntu 12.04.2 LTS) / x86_64  OK  ERROR 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ ERROR ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  ERROR  OK 

Summary

Package: RNAseqData.HeLa.bam.chr14
Version: 0.1.6
Command: rm -rf RNAseqData.HeLa.bam.chr14.buildbin-libdir && mkdir RNAseqData.HeLa.bam.chr14.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAseqData.HeLa.bam.chr14.buildbin-libdir RNAseqData.HeLa.bam.chr14_0.1.6.tar.gz >RNAseqData.HeLa.bam.chr14-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=RNAseqData.HeLa.bam.chr14.buildbin-libdir --install="check:RNAseqData.HeLa.bam.chr14-install.out" --force-multiarch --no-vignettes --timings RNAseqData.HeLa.bam.chr14_0.1.6.tar.gz && mv RNAseqData.HeLa.bam.chr14.buildbin-libdir/* RNAseqData.HeLa.bam.chr14.Rcheck/ && rmdir RNAseqData.HeLa.bam.chr14.buildbin-libdir
StartedAt: 2014-01-06 12:33:33 -0800 (Mon, 06 Jan 2014)
EndedAt: 2014-01-06 12:35:22 -0800 (Mon, 06 Jan 2014)
EllapsedTime: 108.2 seconds
RetCode: 1
Status:  ERROR  
CheckDir: RNAseqData.HeLa.bam.chr14.Rcheck
Warnings: NA

Command output

* using log directory 'E:/biocbld/bbs-2.14-data-experiment/meat/RNAseqData.HeLa.bam.chr14.Rcheck'
* using R Under development (unstable) (2013-12-19 r64488)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNAseqData.HeLa.bam.chr14/DESCRIPTION' ... OK
* this is package 'RNAseqData.HeLa.bam.chr14' version '0.1.6'
* 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 'RNAseqData.HeLa.bam.chr14' can be installed ... WARNING
Found the following significant warnings:
  Warning: 
  Warning: 
See 'E:/biocbld/bbs-2.14-data-experiment/meat/RNAseqData.HeLa.bam.chr14.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'RNAseqData.HNRNPC.bam.chr14'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... 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
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'RNAseqData.HeLa.bam.chr14-package.Rd':
  '[GenomicRanges]{readGAlignmentPairs}'

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.

* 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 ... WARNING
'::' or ':::' import not declared from: 'BiocInstaller'
'library' or 'require' call not declared from: 'Rsamtools'
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'RNAseqData.HeLa.bam.chr14-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RNAseqData.HeLa.bam.chr14-package
> ### Title: Aligned reads from RNAseq experiment: Transcription profiling by
> ###   high throughput sequencing of HNRNPC knockdown and control HeLa cells
> ### Aliases: RNAseqData.HeLa.bam.chr14-package RNAseqData.HeLa.bam.chr14
> ###   RNAseqData.HeLa.bam.chr14_RUNNAMES RNAseqData.HeLa.bam.chr14_BAMFILES
> ### Keywords: package
> 
> ### ** Examples
> 
> RNAseqData.HeLa.bam.chr14_RUNNAMES
[1] "ERR127306" "ERR127307" "ERR127308" "ERR127309" "ERR127302" "ERR127303"
[7] "ERR127304" "ERR127305"
> RNAseqData.HeLa.bam.chr14_BAMFILES
                                                                                   ERR127306 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127306_chr14.bam" 
                                                                                   ERR127307 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127307_chr14.bam" 
                                                                                   ERR127308 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127308_chr14.bam" 
                                                                                   ERR127309 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127309_chr14.bam" 
                                                                                   ERR127302 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127302_chr14.bam" 
                                                                                   ERR127303 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127303_chr14.bam" 
                                                                                   ERR127304 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127304_chr14.bam" 
                                                                                   ERR127305 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127305_chr14.bam" 
> 
> if (require(Rsamtools)) {
+     bamfiles <- RNAseqData.HeLa.bam.chr14_BAMFILES
+     param <- ScanBamParam(tag="NM")
+     if (BiocInstaller:::BIOC_VERSION >= 2.13)
+       func <- readGAlignmentPairs
+     else
+       func <- readGappedAlignmentPairs
+     galp <- func(bamfiles[1L], use.names=TRUE, param=param)
+     galp
+ 
+     first(galp)  # 1st segment in each pair
+     last(galp)  # 2nd segment in each pair
+ 
+     ## The alignments contain insertions, deletions, and gaps (I, D,
+     ## and N CIGAR operations, respectively):
+     colSums(cigarOpTable(cigar(first(galp))))
+     colSums(cigarOpTable(cigar(last(galp))))
+ 
+     ## ngap() returns the nb of gaps for each alignment:
+     table(ngap(first(galp)))
+     table(ngap(last(galp)))
+     table(ngap(first(galp)) + ngap(last(galp)))  # up to 5 gaps per pair!
+ 
+     ## The NM tag gives the edit distance of each alignment to the
+     ## reference (ignoring the gaps):
+     table(mcols(first(galp))$NM)
+     table(mcols(last(galp))$NM)
+     table(mcols(first(galp))$NM + mcols(last(galp))$NM)
+ }
Loading required package: Rsamtools
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
    eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unlist

Loading required package: GenomicRanges
Loading required package: XVector
Loading required package: Biostrings
Error: object 'readGAlignmentPairs' not found
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'RNAseqData.HeLa.bam.chr14-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RNAseqData.HeLa.bam.chr14-package
> ### Title: Aligned reads from RNAseq experiment: Transcription profiling by
> ###   high throughput sequencing of HNRNPC knockdown and control HeLa cells
> ### Aliases: RNAseqData.HeLa.bam.chr14-package RNAseqData.HeLa.bam.chr14
> ###   RNAseqData.HeLa.bam.chr14_RUNNAMES RNAseqData.HeLa.bam.chr14_BAMFILES
> ### Keywords: package
> 
> ### ** Examples
> 
> RNAseqData.HeLa.bam.chr14_RUNNAMES
[1] "ERR127306" "ERR127307" "ERR127308" "ERR127309" "ERR127302" "ERR127303"
[7] "ERR127304" "ERR127305"
> RNAseqData.HeLa.bam.chr14_BAMFILES
                                                                                   ERR127306 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127306_chr14.bam" 
                                                                                   ERR127307 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127307_chr14.bam" 
                                                                                   ERR127308 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127308_chr14.bam" 
                                                                                   ERR127309 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127309_chr14.bam" 
                                                                                   ERR127302 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127302_chr14.bam" 
                                                                                   ERR127303 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127303_chr14.bam" 
                                                                                   ERR127304 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127304_chr14.bam" 
                                                                                   ERR127305 
"E:/biocbld/bbs-2.14-bioc/R/library/RNAseqData.HNRNPC.bam.chr14/extdata/ERR127305_chr14.bam" 
> 
> if (require(Rsamtools)) {
+     bamfiles <- RNAseqData.HeLa.bam.chr14_BAMFILES
+     param <- ScanBamParam(tag="NM")
+     if (BiocInstaller:::BIOC_VERSION >= 2.13)
+       func <- readGAlignmentPairs
+     else
+       func <- readGappedAlignmentPairs
+     galp <- func(bamfiles[1L], use.names=TRUE, param=param)
+     galp
+ 
+     first(galp)  # 1st segment in each pair
+     last(galp)  # 2nd segment in each pair
+ 
+     ## The alignments contain insertions, deletions, and gaps (I, D,
+     ## and N CIGAR operations, respectively):
+     colSums(cigarOpTable(cigar(first(galp))))
+     colSums(cigarOpTable(cigar(last(galp))))
+ 
+     ## ngap() returns the nb of gaps for each alignment:
+     table(ngap(first(galp)))
+     table(ngap(last(galp)))
+     table(ngap(first(galp)) + ngap(last(galp)))  # up to 5 gaps per pair!
+ 
+     ## The NM tag gives the edit distance of each alignment to the
+     ## reference (ignoring the gaps):
+     table(mcols(first(galp))$NM)
+     table(mcols(last(galp))$NM)
+     table(mcols(first(galp))$NM + mcols(last(galp))$NM)
+ }
Loading required package: Rsamtools
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
    eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unlist

Loading required package: GenomicRanges
Loading required package: XVector
Loading required package: Biostrings
Error: object 'readGAlignmentPairs' not found
Execution halted

RNAseqData.HeLa.bam.chr14.Rcheck/00install.out:


install for i386

* installing *source* package 'RNAseqData.HeLa.bam.chr14' ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: 
                    * * * * * * * * * * * * * * * * * * * *
 The RNAseqData.HeLa.bam.chr14 package was renamed RNAseqData.HNRNPC.bam.chr14.
        RNAseqData.HeLa.bam.chr14 is still available but is DEPRECATED.
          Please use the RNAseqData.HNRNPC.bam.chr14 package instead.
                    * * * * * * * * * * * * * * * * * * * *

install for x64

* installing *source* package 'RNAseqData.HeLa.bam.chr14' ...
** testing if installed package can be loaded
Warning: 
                    * * * * * * * * * * * * * * * * * * * *
 The RNAseqData.HeLa.bam.chr14 package was renamed RNAseqData.HNRNPC.bam.chr14.
        RNAseqData.HeLa.bam.chr14 is still available but is DEPRECATED.
          Please use the RNAseqData.HNRNPC.bam.chr14 package instead.
                    * * * * * * * * * * * * * * * * * * * *
* MD5 sums
packaged installation of 'RNAseqData.HeLa.bam.chr14' as RNAseqData.HeLa.bam.chr14_0.1.6.zip
* DONE (RNAseqData.HeLa.bam.chr14)