r3Cseq 1.4.0
Supat Thongjuea
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/r3Cseq | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/r3Cseq.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'r3Cseq/DESCRIPTION' ... OK
* this is package 'r3Cseq' version '1.4.0'
* 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 whether package 'r3Cseq' 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 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
* 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 ... WARNING
'library' or 'require' calls not declared from:
'BSgenome.Hsapiens.UCSC.hg18' 'BSgenome.Hsapiens.UCSC.hg19'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotInteractionsNearViewpoint,r3Cseq: warning in axis(1, at = c(-5e+06,
-4e+06, -3e+06, -2e+06, -1e+06, 0, 1e+06, 2e+06, 3e+06, 4e+06,
5e+06), lab = c(-5, -4, -3, -2, -1, 0, 1, 2, 3, 4, 5)): partial
argument match of 'lab' to 'labels'
plotInteractionsNearViewpoint,r3Cseq: warning in axis(1, at = c(-5e+05,
-4e+05, -3e+05, -2e+05, -1e+05, 0, 1e+05, 2e+05, 3e+05, 4e+05,
5e+05), lab = c(-0.5, -0.4, -0.3, -0.2, -0.1, 0, 0.1, 0.2, 0.3, 0.4,
0.5)): partial argument match of 'lab' to 'labels'
plotInteractionsNearViewpoint,r3Cseq: warning in axis(1, at =
c(-250000, -2e+05, -150000, -1e+05, -50000, 0, 50000, 1e+05, 150000,
2e+05, 250000), lab = c(-2.5, -2, -1.5, -1, -0.5, 0, 0.5, 1, 1.5, 2,
2.5)): partial argument match of 'lab' to 'labels'
plotInteractionsNearViewpoint,r3Cseq: warning in axis(1, at = c(-50000,
-40000, -30000, -20000, -10000, 0, 10000, 20000, 30000, 40000,
50000), lab = c(-5, -4, -3, -2, -1, 0, 1, 2, 3, 4, 5)): partial
argument match of 'lab' to 'labels'
plotOverviewInteractions,r3Cseq: warning in axis(1, at = (seq(0,
max.scale * 10^6, by = 10 * 10^6)), lab = c(seq(0, max.scale, by =
10)), cex.axis = 0.8): partial argument match of 'lab' to 'labels'
getCoverage,r3Cseq: no visible binding for global variable 'Hsapiens'
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable 'Hsapiens'
getEnzymeRestrictionSequences,repbaseEnzyme-character: no visible
binding for global variable 'enzyme'
plotInteractionsPerChromosome,r3Cseq: no visible binding for global
variable 'Hsapiens'
plotOverviewInteractions,r3Cseq: no visible binding for global variable
'Hsapiens'
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following directories should probably not be installed:
'images'
Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getReadCountPerRestrictionFragment 17.169 1.907 19.596
generate3CseqReport 7.066 0.112 7.270
getCoverage 5.540 0.234 5.881
* 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.
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/r3Cseq.Rcheck/00check.log'
for details.