chipseq 1.2.0
Biocore Team c/o BioC user list
| Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/chipseq | | Last Changed Rev: 54800 / Revision: 59457 | | Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ WARNINGS ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/chipseq.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chipseq/DESCRIPTION' ... OK
* this is package 'chipseq' version '1.2.0'
* checking package namespace 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 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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' ... WARNING
Package vignette(s) without corresponding PDF:
Workflow.Rnw
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 2 warnings, see
'D:/biocbld/bbs-2.8-bioc/meat/chipseq.Rcheck/00check.log'
for details
* installing *source* package 'chipseq' ...
** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -O2 -Wall -std=gnu99 -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
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o chipseq.dll tmp.def rlesumprod.o -LD:/biocbld/BBS-2˜1.8-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.8-bioc/meat/chipseq.Rcheck/chipseq/libs/x64
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (chipseq)