Olli-Pekka Huovilainen
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/pint |
| Branch: master |
| Last Commit: 7a6b346 |
| Last Changed Date: 2018-10-30 11:54:28 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:57:51 -0400 (Tue, 09 Apr 2019).
| Package 1192/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pint 1.33.0 Olli-Pekka Huovilainen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: pint |
| Version: 1.33.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pint.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pint_1.33.0.tar.gz |
| StartedAt: 2019-04-09 04:56:50 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:00:45 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 234.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pint.Rcheck |
| Warnings: 0 |
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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:pint.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pint_1.33.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/pint.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 'pint/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pint' version '1.33.0'
* 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 'pint' 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:
'Matrix' 'methods' 'mvtnorm'
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 ... NOTE
Found the following apparent S3 methods exported but not registered:
plot.ChromosomeModels plot.GeneDependencyModel plot.GenomeModels
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
W.effects: no visible global function definition for 'princomp'
W.effects: no visible global function definition for 'cor'
calculate.arm: no visible global function definition for 'as'
calculate.arm: no visible global function definition for 'new'
calculate.arm.sparse: no visible global function definition for 'new'
calculate.chr: no visible global function definition for 'new'
calculate.chr.sparse: no visible global function definition for 'new'
calculate.genome: no visible global function definition for 'new'
calculate.genome.sparse: no visible global function definition for
'new'
imputation: no visible global function definition for 'rnorm'
imputation: no visible global function definition for 'sd'
join.top.regions: no visible global function definition for 'quantile'
plot.ChromosomeModels: no visible global function definition for 'par'
plot.ChromosomeModels: no visible global function definition for
'abline'
plot.ChromosomeModels: no visible global function definition for
'points'
plot.ChromosomeModels: no visible global function definition for 'text'
plot.ChromosomeModels: no visible global function definition for
'lines'
plot.GeneDependencyModel: no visible global function definition for
'gray'
plot.GeneDependencyModel: no visible global function definition for
'par'
plot.GeneDependencyModel: no visible global function definition for
'layout'
plot.GeneDependencyModel: no visible global function definition for
'barplot'
plot.GeneDependencyModel: no visible global function definition for
'legend'
plot.GeneDependencyModel: no visible global function definition for
'mtext'
plot.GenomeModels: no visible global function definition for 'par'
plot.GenomeModels: no visible global function definition for 'abline'
plot.GenomeModels: no visible global function definition for 'points'
plot.GenomeModels: no visible global function definition for 'text'
plot.GenomeModels: no visible global function definition for 'lines'
plot.GenomeModels: no visible global function definition for 'axis'
summarize.region.parameters: no visible global function definition for
'na.omit'
summarize.region.parameters: no visible global function definition for
'cor'
z.effects: no visible global function definition for 'princomp'
coerce,GeneDependencyModel-DependencyModel: no visible global function
definition for 'new'
coerce<-,GeneDependencyModel-DependencyModel: no visible global
function definition for 'slot<-'
coerce<-,GeneDependencyModel-DependencyModel: no visible global
function definition for 'slot'
getPArm,ChromosomeModels: no visible global function definition for
'new'
getQArm,ChromosomeModels: no visible global function definition for
'new'
Undefined global functions or variables:
abline as axis barplot cor gray layout legend lines mtext na.omit new
par points princomp quantile rnorm sd slot slot<- text
Consider adding
importFrom("grDevices", "gray")
importFrom("graphics", "abline", "axis", "barplot", "layout", "legend",
"lines", "mtext", "par", "points", "text")
importFrom("methods", "as", "new", "slot", "slot<-")
importFrom("stats", "cor", "na.omit", "princomp", "quantile", "rnorm",
"sd")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
screen 32.72 0.02 32.73
ChromosomeModels-class 30.28 0.03 30.32
plot 8.74 0.00 8.74
GeneDependencyModel-class 7.67 0.00 7.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
screen 35.42 0.03 35.46
ChromosomeModels-class 27.47 0.06 27.53
plot 10.42 0.02 10.44
GeneDependencyModel-class 8.94 0.00 9.07
* 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-3.9-bioc/meat/pint.Rcheck/00check.log'
for details.
pint.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/pint_1.33.0.tar.gz && rm -rf pint.buildbin-libdir && mkdir pint.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pint.buildbin-libdir pint_1.33.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL pint_1.33.0.zip && rm pint_1.33.0.tar.gz pint_1.33.0.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 340k 100 340k 0 0 5110k 0 --:--:-- --:--:-- --:--:-- 5674k
install for i386
* installing *source* package 'pint' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'pint'
finding HTML links ... done
ChromosomeModels-class html
GeneDependencyModel-class html
finding level-2 HTML links ... done
GenomeModels-class html
fit.byname html
geneCopyNum html
geneExp html
get.neighboring.probes html
get.neighs html
join.top.regions html
order.feature.info html
pint.data html
plot html
screen html
summarize.region.parameters html
window html
z.effect 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 'pint' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pint' as pint_1.33.0.zip
* DONE (pint)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'pint' successfully unpacked and MD5 sums checked
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pint.Rcheck/examples_i386/pint-Ex.timings
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pint.Rcheck/examples_x64/pint-Ex.timings
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