motifRG 1.13.0
Zizhen Yao
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/motifRG | | Last Changed Rev: 102594 / Revision: 107696 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ ERROR ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifRG_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/motifRG.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifRG/DESCRIPTION’ ... OK
* this is package ‘motifRG’ version ‘1.13.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘Biostrings’ ‘IRanges’ ‘seqLogo’ ‘parallel’ ‘grid’ ‘BSgenome’
‘XVector’ ‘BSgenome.Hsapiens.UCSC.hg19’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘motifRG’ can be installed ... [21s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biostrings’ ‘IRanges’ ‘seqLogo’ ‘parallel’ ‘methods’ ‘grid’ ‘graphics’ ‘XVector’
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
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘parallel’ which was already attached by Depends.
Please remove these calls from your code.
Namespaces in Imports field not imported from:
‘graphics’ ‘methods’
All declared Imports should be used.
Packages in Depends field not imported from:
‘BSgenome.Hsapiens.UCSC.hg19’ ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bestPWMMatch: no visible global function definition for ‘Rle’
matchPWMCoor: no visible global function definition for ‘GRanges’
* checking Rd files ... NOTE
prepare_Rd: YY1.control.Rd:8-9: Dropping empty section \details
prepare_Rd: YY1.peak.Rd:8-9: Dropping empty section \details
* 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘motifRG-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: findMotif
> ### Title: De-novo discovery of distriminative motifs
> ### Aliases: findMotif
>
> ### ** Examples
>
> MD.peak.seq <- readDNAStringSet(system.file("extdata","MD.peak.fa", package="motifRG"))
> MD.control.seq <- readDNAStringSet(system.file("extdata","MD.control.fa", package="motifRG"))
> category <- c(rep(1, length(MD.peak.seq)), rep(0, length(MD.control.seq)))
> MD.motifs <- findMotif(append(MD.peak.seq, MD.control.seq),category, max.motif=3,enriched=TRUE)
ACAGCT 2.092662e-07
Refine ACAGCT 15.98224 : 15.99418 15.9742 15.14624 16.36982 15.46506 TRUE 771 155 519 138
ACAGCTR 16.19857 : 15.49232 16.89654 16.81269 16.74783 16.68516 663 78
NCAGCTR 22.10959 : 22.46266 22.27378 22.05622 21.33048 21.82971 1903 272
New motif: CAGCTR
match range 1191
[1] "Rescore"
[1] "Finished Rescore"
CAGCAG 4.415237e-05
Refine CAGCAG 9.862696 : 10.52803 9.022453 9.075196 11.23716 11.61981 TRUE 481 160 340 137
CAGCHG 10.96272 : 12.07607 11.27198 11.78086 12.2132 11.30306 572 179
New motif: CAGCHG
match range 693
[1] "Rescore"
[1] "Finished Rescore"
CACCTG 2.099323e-06
Skip pattern TTAAAA AAAAGA AAAAAT ATAAAA AAAATA TAAAAA
Refine CACCTG 8.185159 : 7.78222 8.051664 8.065775 8.196959 8.965273 TRUE 393 176 320 161
CACCTGNY 10.0786 : 9.236909 10.15766 10.44177 10.75766 9.648679 300 75
CAHCTGNY 12.92609 : 13.58019 12.50839 12.8698 12.67699 11.84033 611 191
CRHCTGNY 13.2656 : 13.89905 13.00029 14.05566 12.89892 13.57512 693 231
New motif: CRHCTGNY
>
> ### Get summary of motifs
> summaryMotif(MD.motifs$motifs, MD.motifs$category)
Warning: non-unique value when setting 'row.names': ‘NNCAGCTGNN’
Error in `row.names<-.data.frame`(`*tmp*`, value = c("NNCAGCTGNN", "NNCAGCTGNN", :
duplicate 'row.names' are not allowed
Calls: summaryMotif -> row.names<- -> row.names<-.data.frame
Execution halted
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/motifRG.Rcheck/00check.log’
for details.