Charles Warden
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/sRAP |
| Branch: master |
| Last Commit: f886f41 |
| Last Changed Date: 2018-10-30 11:54:32 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:13:25 -0400 (Tue, 09 Apr 2019).
| Package 1550/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sRAP 1.23.0 Charles Warden
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: sRAP |
| Version: 1.23.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sRAP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings sRAP_1.23.0.tar.gz |
| StartedAt: 2019-04-09 06:09:43 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 06:14:43 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 299.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: sRAP.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sRAP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings sRAP_1.23.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/sRAP.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sRAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sRAP' version '1.23.0'
* 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 'sRAP' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RNA.bdfunc.fc: no visible global function definition for 'data'
RNA.bdfunc.fc: no visible binding for global variable
'bdfunc.enrichment.human'
RNA.bdfunc.fc: no visible binding for global variable
'bdfunc.enrichment.mouse'
RNA.bdfunc.fc: no visible global function definition for 'read.table'
RNA.bdfunc.fc: no visible global function definition for 'pdf'
RNA.bdfunc.fc: no visible global function definition for 'density'
RNA.bdfunc.fc: no visible global function definition for 'lines'
RNA.bdfunc.fc: no visible global function definition for 'legend'
RNA.bdfunc.fc: no visible global function definition for 'dev.off'
RNA.bdfunc.fc: no visible global function definition for 'p.adjust'
RNA.bdfunc.fc: no visible global function definition for 'write.table'
RNA.bdfunc.signal: no visible global function definition for 'colors'
RNA.bdfunc.signal: no visible global function definition for
'read.table'
RNA.bdfunc.signal: no visible global function definition for 'data'
RNA.bdfunc.signal: no visible binding for global variable
'bdfunc.enrichment.human'
RNA.bdfunc.signal: no visible binding for global variable
'bdfunc.enrichment.mouse'
RNA.bdfunc.signal: no visible global function definition for 'aov'
RNA.bdfunc.signal: no visible global function definition for 'median'
RNA.bdfunc.signal: no visible global function definition for 'pdf'
RNA.bdfunc.signal: no visible global function definition for 'boxplot'
RNA.bdfunc.signal: no visible global function definition for 'dev.off'
RNA.bdfunc.signal: no visible global function definition for 'slot'
RNA.bdfunc.signal: no visible global function definition for 'p.adjust'
RNA.bdfunc.signal: no visible global function definition for
'write.table'
RNA.deg: no visible global function definition for 'colors'
RNA.deg: no visible global function definition for 'read.table'
RNA.deg: no visible global function definition for 'p.adjust'
RNA.deg: no visible global function definition for 'na.omit'
RNA.deg: no visible global function definition for 'pdf'
RNA.deg: no visible global function definition for 'boxplot'
RNA.deg: no visible global function definition for 'dev.off'
RNA.norm: no visible global function definition for 'read.table'
RNA.qc: no visible global function definition for 'colors'
RNA.qc: no visible global function definition for 'read.table'
RNA.qc: no visible global function definition for 'pdf'
RNA.qc: no visible global function definition for 'quantile'
RNA.qc: no visible global function definition for 'density'
RNA.qc: no visible global function definition for 'legend'
RNA.qc: no visible global function definition for 'lines'
RNA.qc: no visible global function definition for 'dev.off'
RNA.qc: no visible global function definition for 'write.table'
RNA.qc: no visible global function definition for 'dist'
RNA.qc: no visible global function definition for 'hclust'
RNA.qc: no visible global function definition for 'as.dendrogram'
RNA.qc: no visible global function definition for 'dendrapply'
RNA.qc: no visible global function definition for 'par'
RNA.qc: no visible global function definition for 'boxplot'
RNA.qc: no visible global function definition for 'prcomp'
RNA.qc: no visible global function definition for 'na.omit'
annova.pvalue: no visible global function definition for 'aov'
colLab: no visible global function definition for 'is.leaf'
ks.est: no visible global function definition for 'ks.test'
ks.pvalue: no visible global function definition for 'ks.test'
lm.annova.pvalue: no visible global function definition for 'lm'
lm.annova.pvalue: no visible global function definition for 'anova'
mwu.est: no visible global function definition for 'wilcox.test'
mwu.pvalue: no visible global function definition for 'wilcox.test'
ttest.est: no visible global function definition for 't.test'
ttest.pvalue: no visible global function definition for 't.test'
Undefined global functions or variables:
anova aov as.dendrogram bdfunc.enrichment.human
bdfunc.enrichment.mouse boxplot colors data dendrapply density
dev.off dist hclust is.leaf ks.test legend lines lm median na.omit
p.adjust par pdf prcomp quantile read.table slot t.test wilcox.test
write.table
Consider adding
importFrom("grDevices", "colors", "dev.off", "pdf")
importFrom("graphics", "boxplot", "legend", "lines", "par")
importFrom("methods", "slot")
importFrom("stats", "anova", "aov", "as.dendrogram", "dendrapply",
"density", "dist", "hclust", "is.leaf", "ks.test", "lm",
"median", "na.omit", "p.adjust", "prcomp", "quantile",
"t.test", "wilcox.test")
importFrom("utils", "data", "read.table", "write.table")
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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
bdfunc.enrichment.human.rda 1.3Mb 951Kb bzip2
bdfunc.enrichment.mouse.rda 31Kb 26Kb xz
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RNA.bdfunc.signal 82.47 0.03 87.70
RNA.bdfunc.fc 11.14 0.13 16.72
RNA.deg 7.80 0.01 12.80
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RNA.bdfunc.signal 77.87 0.05 83.49
RNA.bdfunc.fc 10.10 0.00 15.73
RNA.deg 9.58 0.03 19.56
* 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 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/sRAP.Rcheck/00check.log'
for details.
sRAP.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/sRAP_1.23.0.tar.gz && rm -rf sRAP.buildbin-libdir && mkdir sRAP.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sRAP.buildbin-libdir sRAP_1.23.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL sRAP_1.23.0.zip && rm sRAP_1.23.0.tar.gz sRAP_1.23.0.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
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100 1775k 100 1775k 0 0 3067k 0 --:--:-- --:--:-- --:--:-- 3098k
install for i386
* installing *source* package 'sRAP' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'sRAP'
finding HTML links ... done
RNA.bdfunc.fc html
RNA.bdfunc.signal html
RNA.deg html
RNA.norm html
RNA.prepare.input html
RNA.qc html
bdfunc.enrichment.human html
bdfunc.enrichment.mouse html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'sRAP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sRAP' as sRAP_1.23.0.zip
* DONE (sRAP)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'sRAP' successfully unpacked and MD5 sums checked
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sRAP.Rcheck/examples_i386/sRAP-Ex.timings
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sRAP.Rcheck/examples_x64/sRAP-Ex.timings
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