Lin Zhang
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/exomePeak |
| Branch: RELEASE_3_7 |
| Last Commit: cb8a459 |
| Last Changed Date: 2018-04-30 10:35:31 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:37:48 -0400 (Wed, 17 Oct 2018).
| Package 468/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| exomePeak 2.14.0 Lin Zhang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: exomePeak |
| Version: 2.14.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:exomePeak.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings exomePeak_2.14.0.tar.gz |
| StartedAt: 2018-10-17 01:54:33 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:59:11 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 278.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: exomePeak.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:exomePeak.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings exomePeak_2.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/exomePeak.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'exomePeak/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'exomePeak' version '2.14.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'exomePeak' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
'GenomicAlignments' 'GenomicFeatures' 'Rsamtools' 'rtracklayer'
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
.bed2grangeslist: no visible global function definition for 'head'
.bed2grangeslist: no visible global function definition for 'makeTxDb'
.bed2grangeslist: no visible global function definition for 'exonsBy'
.exomepeak_notification: no visible global function definition for
'mcols<-'
.get.bam.chrs: no visible global function definition for 'indexBam'
.get.bam.chrs: no visible global function definition for 'ScanBamParam'
.get.bam.chrs: no visible global function definition for 'scanBam'
.get.bam.read.length: no visible global function definition for
'indexBam'
.get.bam.read.length: no visible global function definition for
'ScanBamParam'
.get.bam.read.length: no visible global function definition for
'scanBam'
.get.bam.read.length: no visible global function definition for
'median'
.get.check.points.reads.count: no visible global function definition
for 'IRangesList'
.get.check.points.reads.count: no visible global function definition
for 'IRanges'
.get.check.points.reads.count: no visible global function definition
for 'ScanBamParam'
.get.check.points.reads.count: no visible global function definition
for 'scanBam'
.read.gtf: no visible global function definition for 'makeTxDbFromUCSC'
.read.gtf: no visible global function definition for 'makeTxDbFromGFF'
.read.gtf: no visible global function definition for 'columns'
.read.gtf: no visible global function definition for 'keys'
.read.gtf: no visible global function definition for 'select'
.readTxDb2: no visible global function definition for
'makeTxDbFromUCSC'
.readTxDb2: no visible global function definition for 'makeTxDbFromGFF'
.report.diff.peak.based.on.result: no visible global function
definition for 'write.table'
.report.peak.based.on.result: no visible global function definition for
'write.table'
.xls2Grangeslist: no visible global function definition for
'read.table'
.xls2Grangeslist: no visible global function definition for 'head'
.xls2Grangeslist: no visible global function definition for 'makeTxDb'
.xls2Grangeslist: no visible global function definition for 'exonsBy'
.xls2Grangeslist: no visible global function definition for 'mcols<-'
RMT: no visible global function definition for 'read.table'
RMT: no visible global function definition for 'write.table'
RMT: no visible global function definition for 'findOverlaps'
RMT: no visible global function definition for 'queryHits'
RMT: no visible global function definition for 'subjectHits'
RMT: no visible global function definition for 'ranges'
RMT: no visible global function definition for 'exonsBy'
RMT: no visible global function definition for 'readGAlignments'
RMT: no visible global function definition for 'ScanBamParam'
RMT: no visible global function definition for 'scanBam'
RMT: no visible global function definition for 'countOverlaps'
RMT: no visible global function definition for 'width'
RMT: no visible global function definition for 'var'
bltest: no visible global function definition for 'pchisq'
bltest: no visible global function definition for 'p.adjust'
ctest: no visible global function definition for 'pbinom'
ctest: no visible global function definition for 'p.adjust'
exomepeak: no visible global function definition for 'indexBam'
rhtest: no visible global function definition for 'phyper'
rhtest: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
IRanges IRangesList ScanBamParam columns countOverlaps exonsBy
findOverlaps head indexBam keys makeTxDb makeTxDbFromGFF
makeTxDbFromUCSC mcols<- median p.adjust pbinom pchisq phyper
queryHits ranges read.table readGAlignments scanBam select
subjectHits var width write.table
Consider adding
importFrom("stats", "median", "p.adjust", "pbinom", "pchisq", "phyper",
"var")
importFrom("utils", "head", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: RMT.Rd:60-62: Dropping empty section \details
prepare_Rd: RMT.Rd:74-76: Dropping empty section \note
prepare_Rd: RMT.Rd:80-82: Dropping empty section \seealso
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RMT 23.15 0.50 25.55
exomepeak 10.49 0.12 11.99
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RMT 21.07 0.14 21.22
exomepeak 8.63 0.11 8.73
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/exomePeak.Rcheck/00check.log'
for details.
exomePeak.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/exomePeak_2.14.0.tar.gz && rm -rf exomePeak.buildbin-libdir && mkdir exomePeak.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=exomePeak.buildbin-libdir exomePeak_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL exomePeak_2.14.0.zip && rm exomePeak_2.14.0.tar.gz exomePeak_2.14.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2153k 100 2153k 0 0 19.4M 0 --:--:-- --:--:-- --:--:-- 20.6M
install for i386
* installing *source* package 'exomePeak' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'exomePeak'
finding HTML links ... done
RMT html
bltest html
ctest html
exomePeak-package html
exomepeak html
rhtest html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'exomePeak' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'exomePeak' as exomePeak_2.14.0.zip
* DONE (exomePeak)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'exomePeak' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
exomePeak.Rcheck/examples_i386/exomePeak-Ex.timings
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exomePeak.Rcheck/examples_x64/exomePeak-Ex.timings
|