Sebastien Artigaud
| Snapshot Date: 2018-10-28 16:46:29 -0400 (Sun, 28 Oct 2018) |
| URL: https://git.bioconductor.org/packages/prot2D |
| Branch: master |
| Last Commit: 5455c7c |
| Last Changed Date: 2018-09-24 12:18:06 -0400 (Mon, 24 Sep 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2018-10-29 10:26:12 -0400 (Mon, 29 Oct 2018).
| Package 1199/1642 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Sebastien Artigaud
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: prot2D |
| Version: 1.19.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:prot2D.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings prot2D_1.19.1.tar.gz |
| StartedAt: 2018-10-29 05:43:35 -0400 (Mon, 29 Oct 2018) |
| EndedAt: 2018-10-29 05:45:42 -0400 (Mon, 29 Oct 2018) |
| EllapsedTime: 126.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: prot2D.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:prot2D.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings prot2D_1.19.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/prot2D.Rcheck'
* using R Under development (unstable) (2018-10-22 r75479)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'prot2D/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'prot2D' version '1.19.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'fdrtool', 'st', 'samr', 'Biobase', 'limma', 'Mulcom', 'impute',
'MASS', 'qvalue'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'prot2D' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpe43ghl/R.INSTALL14d02ad498/prot2D/man/prot2D-package.Rd:14: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpe43ghl/R.INSTALL14d02ad498/prot2D/man/prot2D-package.Rd:15: file link 'modT.Prot' in package 'prot2D' does not exist and so has been treated as a topic
Warning: Package 'prot2D' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/prot2D.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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:
'MASS' 'fdrtool' 'limma' 'samr' 'st'
Please remove these calls from your code.
Packages in Depends field not imported from:
'MASS' 'Mulcom' 'impute'
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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ES.prot: no visible global function definition for 'new'
Norm.qt: no visible global function definition for 'normalizeQuantiles'
Norm.qt: no visible global function definition for 'par'
Norm.vsn: no visible global function definition for 'normalizeVSN'
Norm.vsn: no visible global function definition for 'par'
RIplot: no visible global function definition for 'plot'
RIplot: no visible global function definition for 'grey'
RIplot: no visible global function definition for 'abline'
RIplot: no visible global function definition for 'points'
RIplot: no visible global function definition for 'text'
Sim.Prot.2D: no visible global function definition for 'rchisq'
Sim.Prot.2D: no visible global function definition for 'runif'
Sim.Prot.2D: no visible global function definition for 'rnorm'
efronT.Prot: no visible global function definition for 'abline'
modT.Prot: no visible global function definition for 'abline'
robust.fdr : lts.rank.regr: no visible global function definition for
'ltsreg'
robust.fdr : lts.rank.regr: no visible global function definition for
'approx'
robust.fdr: no visible global function definition for 'approx'
samT.Prot: no visible global function definition for 'abline'
shrinkT.Prot: no visible global function definition for 'abline'
ttest.Prot: no visible global function definition for 'abline'
Undefined global functions or variables:
abline approx grey ltsreg new normalizeQuantiles normalizeVSN par
plot points rchisq rnorm runif text
Consider adding
importFrom("grDevices", "grey")
importFrom("graphics", "abline", "par", "plot", "points", "text")
importFrom("methods", "new")
importFrom("stats", "approx", "rchisq", "rnorm", "runif")
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
** 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: 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/prot2D.Rcheck/00check.log'
for details.
prot2D.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/prot2D_1.19.1.tar.gz && rm -rf prot2D.buildbin-libdir && mkdir prot2D.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=prot2D.buildbin-libdir prot2D_1.19.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL prot2D_1.19.1.zip && rm prot2D_1.19.1.tar.gz prot2D_1.19.1.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'prot2D' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'prot2D'
finding HTML links ... done
ES.prot html
finding level-2 HTML links ... done
Norm.qt html
Norm.vsn html
RIplot html
Sim.Prot.2D html
pecten html
pecten.fac html
prot2D-package html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpe43ghl/R.INSTALL14d02ad498/prot2D/man/prot2D-package.Rd:14: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpe43ghl/R.INSTALL14d02ad498/prot2D/man/prot2D-package.Rd:15: file link 'modT.Prot' in package 'prot2D' does not exist and so has been treated as a topic
robust.fdr html
variousT html
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'prot2D' is deprecated and will be removed from Bioconductor
version 3.9
In R CMD INSTALL
install for x64
* installing *source* package 'prot2D' ...
** testing if installed package can be loaded
Warning: Package 'prot2D' is deprecated and will be removed from Bioconductor
version 3.9
* MD5 sums
packaged installation of 'prot2D' as prot2D_1.19.1.zip
* DONE (prot2D)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'prot2D' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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prot2D.Rcheck/examples_i386/prot2D-Ex.timings
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prot2D.Rcheck/examples_x64/prot2D-Ex.timings
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