ELMER 1.4.2
Lijing Yao
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/ELMER | | Last Changed Rev: 117513 / Revision: 122332 | | Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ELMER_1.4.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ELMER.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ELMER/DESCRIPTION’ ... OK
* this is package ‘ELMER’ version ‘1.4.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ELMER’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘ELMER.data’ ‘Homo.sapiens’
‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
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
Stat.diff.meth: no visible binding for global variable ‘t.test’
Stat.nonpara : <anonymous>: no visible global function definition for
‘wilcox.test’
Stat.nonpara: no visible global function definition for ‘wilcox.test’
Stat.nonpara.permu : <anonymous>: no visible global function definition
for ‘wilcox.test’
Stat.nonpara.permu: no visible global function definition for
‘write.table’
TCGA.pipe: no visible global function definition for ‘read.csv’
TCGA.pipe: no visible global function definition for ‘write.csv’
TF.rank.plot: no visible global function definition for ‘data’
TF.rank.plot: no visible binding for global variable ‘pvalue’
TF.rank.plot: no visible binding for global variable ‘label’
TF.rank.plot: no visible global function definition for ‘pdf’
TF.rank.plot: no visible global function definition for ‘dev.off’
fetch.pair: no visible global function definition for ‘read.csv’
get.TFs: no visible global function definition for ‘data’
get.TFs: no visible global function definition for ‘read.csv’
get.TFs: no visible global function definition for ‘write.csv’
get.diff.meth: no visible global function definition for ‘p.adjust’
get.diff.meth: no visible global function definition for ‘write.csv’
get.enriched.motif: no visible global function definition for ‘data’
get.enriched.motif: no visible global function definition for
‘write.csv’
get.enriched.motif: no visible global function definition for
‘read.csv’
get.feature.probe: no visible binding for global variable
‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
get.feature.probe: no visible global function definition for ‘data’
get.pair: no visible global function definition for ‘write.csv’
get.pair : <anonymous>: no visible global function definition for
‘t.test’
get.pair : <anonymous>: no visible global function definition for
‘wilcox.test’
get.permu : <anonymous>: no visible global function definition for
‘read.table’
lm_eqn: no visible global function definition for ‘lm’
lm_eqn: no visible global function definition for ‘coef’
matrixClinic: no visible global function definition for ‘read.delim’
matrixMeth: no visible global function definition for ‘read.table’
matrixMeth : <anonymous>: no visible global function definition for
‘read.table’
matrixRNA: no visible global function definition for ‘read.table’
matrixRNA : <anonymous>: no visible global function definition for
‘read.table’
motif.enrichment.plot: no visible global function definition for
‘read.csv’
motif.enrichment.plot: no visible binding for global variable ‘upperOR’
motif.enrichment.plot: no visible binding for global variable ‘lowerOR’
motif.enrichment.plot: no visible binding for global variable ‘motif’
motif.enrichment.plot: no visible binding for global variable ‘OR’
promoterMeth: no visible global function definition for ‘write.csv’
scatter: no visible binding for global variable ‘value’
schematic: no visible global function definition for ‘pdf’
schematic: no visible global function definition for ‘dev.off’
txs: no visible binding for global variable ‘Homo.sapiens’
show,MEE.data: no visible global function definition for ‘str’
show,Pair: no visible global function definition for ‘str’
summary,MEE.data: no visible global function definition for ‘str’
summary,Pair: no visible global function definition for ‘str’
Undefined global functions or variables:
Homo.sapiens IlluminaHumanMethylation450kanno.ilmn12.hg19 OR coef
data dev.off label lm lowerOR motif p.adjust pdf pvalue read.csv
read.delim read.table str t.test upperOR value wilcox.test write.csv
write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("stats", "coef", "lm", "p.adjust", "t.test", "wilcox.test")
importFrom("utils", "data", "read.csv", "read.delim", "read.table",
"str", "write.csv", "write.table")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
get.feature.probe 11.476 1.155 13.225
get.pair 7.866 0.041 7.940
schematic.plot 6.599 0.103 6.819
GetNearGenes 5.688 0.076 5.937
scatter.plot 5.529 0.060 5.612
get.permu 5.087 0.000 5.210
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/ELMER.Rcheck/00check.log’
for details.