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Package 88/464HostnameOS / ArchBUILDCHECKBUILD BIN
chipseq 1.3.0
Biocore Team c/o BioC user list
Snapshot Date: 2011-06-03 07:21:36 -0700 (Fri, 03 Jun 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chipseq
Last Changed Rev: 54802 / Revision: 55980
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
liverpool Windows Server 2003 R2 (32-bit) / x64  ERROR  skipped  skipped 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: chipseq
Version: 1.3.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings chipseq_1.3.0.tar.gz
StartedAt: 2011-06-03 11:46:14 -0700 (Fri, 03 Jun 2011)
EndedAt: 2011-06-03 11:49:48 -0700 (Fri, 03 Jun 2011)
EllapsedTime: 213.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: chipseq.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/chipseq.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-05-30 r56024)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chipseq/DESCRIPTION’ ... OK
* this is package ‘chipseq’ version ‘1.3.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘chipseq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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 ... NOTE
correlation.estimate: no visible binding for global variable ‘mu’
correlation.estimate: no visible binding for global variable ‘corr’
coverage.estimate: no visible binding for global variable ‘mu’
coverage.estimate: no visible binding for global variable ‘covered’
diffPeakSummaryRef: no visible global function definition for
  ‘laneCoverage’
islandDepthPlot: no visible binding for global variable ‘depth’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'estimate.mean.fraglen':
basesCovered
  Code: function(x, shift = seq(5, 300, 5), seqLen = 100, verbose =
                 FALSE)
  Docs: function(x, shift = seq(5, 300, 5), seqLen = 35, verbose =
                 FALSE)
  Mismatches in argument default values:
    Name: 'seqLen' Code: 100 Docs: 35
densityCorr
  Code: function(x, shift = seq(0, 500, 5), center = FALSE, width =
                 seqLen * 2L, seqLen = 100L, ...)
  Docs: function(x, shift = seq(0, 500, 5), center = FALSE, width = 50,
                 ...)
  Argument names in code not in docs:
    seqLen
  Mismatches in argument names:
    Position: 5 Code: seqLen Docs: ...
  Mismatches in argument default values:
    Name: 'width' Code: seqLen * 2L Docs: 50
sparse.density
  Code: function(x, width = 50, kernel = "epanechnikov", from =
                 start(rix)[1] - 10L, to = end(rix)[length(rix)] + 10L)
  Docs: function(x, width = 50, kernel = "epanechnikov", experimental =
                 TRUE, from, to)
  Argument names in docs not in code:
    experimental
  Mismatches in argument names:
    Position: 4 Code: from Docs: experimental
    Position: 5 Code: to Docs: from
  Mismatches in argument default values:
    Name: 'from' Code: start(rix)[1] - 10L Docs: 
    Name: 'to' Code: end(rix)[length(rix)] + 10L Docs: 

* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/chipseq.Rcheck/00check.log’
for details

chipseq.Rcheck/00install.out:

* installing *source* package ‘chipseq’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rlesumprod.c -o rlesumprod.o
rlesumprod.c: In function ‘rle_sum_prod’:
rlesumprod.c:24:16: warning: operation on ‘i1’ may be undefined
rlesumprod.c:25:16: warning: operation on ‘i2’ may be undefined
rlesumprod.c:27:44: warning: operation on ‘i1’ may be undefined
rlesumprod.c:28:44: warning: operation on ‘i2’ may be undefined
rlesumprod.c:34:37: warning: operation on ‘i1’ may be undefined
rlesumprod.c:35:37: warning: operation on ‘i2’ may be undefined
rlesumprod.c: In function ‘rle_sum_any’:
rlesumprod.c:61:33: warning: operation on ‘i1’ may be undefined
rlesumprod.c:62:33: warning: operation on ‘i2’ may be undefined
gcc -std=gnu99 -shared -L/usr/local/lib64 -o chipseq.so rlesumprod.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/chipseq.Rcheck/chipseq/libs
** R
** data
** inst
** preparing package for lazy loading

Attaching package: ‘IRanges’

The following object(s) are masked from ‘package:base’:

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘Workflow.Rnw’ 
** testing if installed package can be loaded

* DONE (chipseq)

chipseq.Rcheck/chipseq-Ex.timings:

nameusersystemelapsed
chipseqFilter0.8120.0120.850
combineLanes15.613 0.16415.787
copyIRangesbyChr0.0160.0000.016
coverageplot0.1320.0080.139
cstest0.2880.0160.306
diffPeakSummary12.765 0.04413.076
estimate.mean.fraglen2.0320.0082.041
extendReads1.6080.0121.617
islandDepthPlot2.7520.0002.751
peakCutoff3.8050.0083.812
readReads000
subsetSummary2.8920.0362.931