SEPA 1.6.0
Zhicheng Ji
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/SEPA | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf SEPA.buildbin-libdir SEPA.Rcheck && mkdir SEPA.buildbin-libdir SEPA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SEPA.buildbin-libdir SEPA_1.6.0.tar.gz >SEPA.Rcheck\00install.out 2>&1 && cp SEPA.Rcheck\00install.out SEPA-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SEPA.buildbin-libdir --install="check:SEPA-install.out" --force-multiarch --no-vignettes --timings SEPA_1.6.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/SEPA.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SEPA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SEPA' version '1.6.0'
* 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 'SEPA' 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
patternGOanalysis: no visible global function definition for 'new'
pseudotimepattern : <anonymous>: no visible global function definition
for 'lm'
pseudotimepattern: no visible global function definition for 'p.adjust'
pseudotimepattern: no visible global function definition for 'lm'
pseudotimepattern: no visible global function definition for 'lines'
pseudotimepattern: no visible global function definition for 'confint'
pseudotimepattern: no visible global function definition for 'fitted'
pseudotimepattern : <anonymous>: no visible global function definition
for 'fitted'
pseudotimevisualize: no visible binding for global variable
'pseudotime'
pseudotimevisualize: no visible binding for global variable 'Var2'
pseudotimevisualize: no visible binding for global variable 'Var1'
pseudotimevisualize: no visible binding for global variable 'value'
pseudotimevisualize: no visible binding for global variable 'xend'
pseudotimevisualize: no visible binding for global variable 'yend'
truetimepattern : <anonymous> : <anonymous>: no visible global function
definition for 't.test'
truetimepattern : <anonymous>: no visible global function definition
for 'p.adjust'
truetimevisualize : <anonymous> : <anonymous>: no visible global
function definition for 'median'
truetimevisualize: no visible binding for global variable 'time'
truetimevisualize: no visible binding for global variable 'expmean'
truetimevisualize: no visible binding for global variable 'Gene'
windowGOanalysis: no visible global function definition for 'new'
windowGOvisualize: no visible binding for global variable 'Var1'
windowGOvisualize: no visible binding for global variable 'value'
Undefined global functions or variables:
Gene Var1 Var2 confint expmean fitted lines lm median new p.adjust
pseudotime t.test time value xend yend
Consider adding
importFrom("graphics", "lines")
importFrom("methods", "new")
importFrom("stats", "confint", "fitted", "lm", "median", "p.adjust",
"t.test", "time")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
windowGOanalysis 110.11 0.25 110.36
windowGOvisualize 104.42 0.39 104.81
pseudotimepattern 87.98 0.41 88.39
pseudotimevisualize 77.23 0.00 77.24
patternGOanalysis 62.26 0.78 63.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
windowGOvisualize 104.67 0.25 104.92
windowGOanalysis 92.23 0.33 92.58
pseudotimepattern 67.93 0.22 68.16
pseudotimevisualize 64.31 0.00 64.31
patternGOanalysis 55.98 0.72 56.71
* 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
'C:/Users/biocbuild/bbs-3.5-bioc/meat/SEPA.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'SEPA' ...
** 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 'SEPA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SEPA' as SEPA_1.6.0.zip
* DONE (SEPA)