Xiaogang Zhong
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/MergeMaid |
| Branch: RELEASE_3_8 |
| Last Commit: 8e79bd2 |
| Last Changed Date: 2018-10-30 11:41:41 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:19:27 -0400 (Sat, 13 Apr 2019).
| Package 908/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MergeMaid 2.54.0 Xiaogang Zhong
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: MergeMaid |
| Version: 2.54.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MergeMaid.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MergeMaid_2.54.0.tar.gz |
| StartedAt: 2019-04-13 03:37:37 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:41:00 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 202.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MergeMaid.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MergeMaid.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MergeMaid_2.54.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MergeMaid.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MergeMaid/DESCRIPTION' ... OK
* this is package 'MergeMaid' version '2.54.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'MergeMaid' 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:
'MASS' 'methods' 'survival'
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
.dens.mergeExpressionSet: no visible global function definition for
'density'
.fdr.mergeCor: no visible global function definition for '.getnull'
.fdr.mergeCor: no visible global function definition for 'approxfun'
.fdr.mergeCor: no visible global function definition for 'density'
.fdr.mergeCor: no visible global function definition for 'integrate'
.ic.plot : norm: no visible global function definition for 'sd'
.ic.plot: no visible global function definition for 'cov'
.icor : norm: no visible global function definition for 'sd'
.icor: no visible global function definition for 'cov'
.intcor : norm: no visible global function definition for 'sd'
.intcor: no visible global function definition for 'new'
.integ.cal : sziicor: no visible global function definition for 'cor'
.mergemodel: no visible global function definition for 'lm'
.mergemodel: no visible binding for global variable 'na.omit'
.mergemodel: no visible global function definition for 'coxph'
.mergemodel: no visible global function definition for 'sd'
.mergemodel: no visible global function definition for 'glm'
.mergemodel: no visible binding for global variable 'binomial'
.model.outcome: no visible global function definition for 'new'
.nullicornorm : norm: no visible global function definition for 'sd'
.nullicornorm: no visible global function definition for 'cov'
.nullicornorm : getone: no visible global function definition for
'rnorm'
maxintcor: no visible global function definition for 'cov'
maxintcor: no visible global function definition for 'ginv'
mergeExprs: no visible global function definition for 'new'
mergeget: no visible global function definition for 'new'
subsetmES: no visible global function definition for 'new'
intersection,mergeExpressionSet: no visible global function definition
for 'new'
Undefined global functions or variables:
.getnull approxfun binomial cor cov coxph density ginv glm integrate
lm na.omit new rnorm sd
Consider adding
importFrom("methods", "new")
importFrom("stats", "approxfun", "binomial", "cor", "cov", "density",
"glm", "integrate", "lm", "na.omit", "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 ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'mergeExpressionSet,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
intcorDens 17.67 0.18 17.86
class.mergeExpressionSet 7.20 0.06 7.27
intCor 5.83 0.02 5.84
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
intcorDens 17.26 0.06 17.33
class.mergeExpressionSet 8.00 0.00 8.00
intCor 5.69 0.00 5.69
* 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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/MergeMaid.Rcheck/00check.log'
for details.
MergeMaid.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MergeMaid_2.54.0.tar.gz && rm -rf MergeMaid.buildbin-libdir && mkdir MergeMaid.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MergeMaid.buildbin-libdir MergeMaid_2.54.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MergeMaid_2.54.0.zip && rm MergeMaid_2.54.0.tar.gz MergeMaid_2.54.0.zip
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install for i386
* installing *source* package 'MergeMaid' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MergeMaid'
finding HTML links ... done
class.mergeCoeff html
class.mergeCor html
class.mergeExpressionSet html
intCor html
intcorDens html
intersection html
mergeData html
mergeExprs html
modelOutcome html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'MergeMaid' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MergeMaid' as MergeMaid_2.54.0.zip
* DONE (MergeMaid)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MergeMaid' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
MergeMaid.Rcheck/examples_i386/MergeMaid-Ex.timings
|
MergeMaid.Rcheck/examples_x64/MergeMaid-Ex.timings
|