Soo-heang Eo
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/PLPE |
| Branch: RELEASE_3_9 |
| Last Commit: dfb47fe |
| Last Changed Date: 2019-05-02 11:53:10 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:22:04 -0400 (Wed, 16 Oct 2019).
| Package 1224/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PLPE 1.44.0 Soo-heang Eo
| 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 | |
| Package: PLPE |
| Version: 1.44.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PLPE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PLPE_1.44.0.tar.gz |
| StartedAt: 2019-10-16 06:02:19 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:03:07 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 47.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PLPE.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:PLPE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PLPE_1.44.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PLPE.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PLPE/DESCRIPTION' ... OK
* this is package 'PLPE' version '1.44.0'
* 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 'PLPE' 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
'library' or 'require' calls to packages already attached by Depends:
'Biobase' 'LPE' 'MASS' 'methods'
Please remove these calls from your code.
Package in Depends field not imported from: 'LPE'
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:
lpe.paired.fdr
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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'PLPE/R/lpe.paired.R':
.First.lib calls:
cat("LPEP version 1.0.0 \n")
require(Biobase)
require(methods)
Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
generate messages.
See section 'Good practice' in '?.onAttach'.
base.error.paired: no visible global function definition for 'na.omit'
base.error.paired: no visible global function definition for 'quantile'
base.error.paired: no visible global function definition for 'var'
base.error.paired: no visible global function definition for 'median'
base.error.paired: no visible global function definition for
'smooth.spline'
base.error.paired: no visible global function definition for
'fixbounds.predict.smooth.spline'
generate.null: no visible global function definition for 'quantile'
generate.null: no visible global function definition for 'median'
lpe.paired.default: no visible binding for global variable 'median'
lpe.paired.default: no visible binding for global variable 'var'
lpe.paired.default: no visible binding for global variable 't.test'
lpe.paired.default: no visible global function definition for 'pnorm'
lpe.paired.default: no visible global function definition for 'lm'
lpe.paired.fdr.default: no visible global function definition for
'quantile'
summary.lpe.paired: no visible global function definition for 'head'
summary.lpe.paired.fdr: no visible global function definition for
'head'
Undefined global functions or variables:
fixbounds.predict.smooth.spline head lm median na.omit pnorm quantile
smooth.spline t.test var
Consider adding
importFrom("stats", "lm", "median", "na.omit", "pnorm", "quantile",
"smooth.spline", "t.test", "var")
importFrom("utils", "head")
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 ... NOTE
S3 methods shown with full name in documentation object 'lpe.paired.fdr':
'lpe.paired.fdr'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
** running examples for arch 'x64' ... 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/PLPE.Rcheck/00check.log'
for details.
PLPE.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/PLPE_1.44.0.tar.gz && rm -rf PLPE.buildbin-libdir && mkdir PLPE.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PLPE.buildbin-libdir PLPE_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PLPE_1.44.0.zip && rm PLPE_1.44.0.tar.gz PLPE_1.44.0.zip
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install for i386
* installing *source* package 'PLPE' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'PLPE'
finding HTML links ... done
am.trans.paired html
base.error.paired html
generate.null html
lpe.paired html
lpe.paired.default html
lpe.paired.fdr html
lpe.paired.fdr.default html
plateletSet html
print.lpe.paired html
print.lpe.paired.fdr html
summary.lpe.paired html
summary.lpe.paired.fdr 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 'PLPE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PLPE' as PLPE_1.44.0.zip
* DONE (PLPE)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PLPE' successfully unpacked and MD5 sums checked
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PLPE.Rcheck/examples_i386/PLPE-Ex.timings
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PLPE.Rcheck/examples_x64/PLPE-Ex.timings
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