isomiRs 1.0.3
Lorena Pantano
| 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/isomiRs | | Last Changed Rev: 118067 / Revision: 122332 | | Last Changed Date: 2016-06-01 10:54:21 -0700 (Wed, 01 Jun 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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### rm -rf isomiRs.buildbin-libdir isomiRs.Rcheck && mkdir isomiRs.buildbin-libdir isomiRs.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=isomiRs.buildbin-libdir isomiRs_1.0.3.tar.gz >isomiRs.Rcheck\00install.out 2>&1 && cp isomiRs.Rcheck\00install.out isomiRs-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=isomiRs.buildbin-libdir --install="check:isomiRs-install.out" --force-multiarch --no-vignettes --timings isomiRs_1.0.3.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/isomiRs.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'isomiRs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'isomiRs' version '1.0.3'
* 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 'isomiRs' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking 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
.clean_low_rate_changes: no visible binding for global variable 'subs'
.clean_low_rate_changes: no visible binding for global variable 'mir'
.clean_low_rate_changes: no visible binding for global variable 'freq'
.clean_low_rate_changes: no visible binding for global variable
'total_subs'
.clean_low_rate_changes: no visible binding for global variable
'total_mir'
.clean_low_rate_changes: no visible binding for global variable 'add'
.clean_low_rate_changes: no visible binding for global variable 't5'
.clean_low_rate_changes: no visible binding for global variable 't3'
.clean_low_rate_changes: no visible binding for global variable 'DB'
.clean_low_rate_changes: no visible binding for global variable
'ambiguity'
.filter_by_cov: no visible binding for global variable 'subs'
IsomirDataSeqFromFiles: no visible global function definition for
'read.table'
isoPLSDAplot: no visible binding for global variable 'condition'
isoPlotPosition: no visible binding for global variable 'reference'
isoPlotPosition: no visible binding for global variable 'current'
isoPlotPosition: no visible binding for global variable 'change'
isoPlotPosition: no visible global function definition for 'n'
isoSelect.IsomirDataSeq : <anonymous>: no visible binding for global
variable 'mir'
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
variable 'mir'
Undefined global functions or variables:
DB add ambiguity change condition current freq mir n read.table
reference subs t3 t5 total_mir total_subs
Consider adding
importFrom("utils", "read.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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
isoDE 5.93 0.01 5.96
isoPLSDAplot 5.77 0.03 5.80
isoNorm 5.46 0.03 5.49
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
isoDE 7.05 0.06 7.25
isoPLSDAplot 5.72 0.06 5.80
isoNorm 5.42 0.05 5.46
isoCounts 5.35 0.06 5.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
OK
* 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 NOTE
See
'E:/biocbld/bbs-3.3-bioc/meat/isomiRs.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'isomiRs' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'isomiRs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'isomiRs' as isomiRs_1.0.3.zip
* DONE (isomiRs)