Benjamin Haibe-Kains
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/genefu |
| Branch: RELEASE_3_8 |
| Last Commit: 0825dec |
| Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:21:36 -0400 (Sat, 13 Apr 2019).
| Package 596/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genefu 2.14.0 Benjamin Haibe-Kains
| 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: genefu |
| Version: 2.14.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genefu.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings genefu_2.14.0.tar.gz |
| StartedAt: 2019-04-13 02:27:43 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:32:37 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 293.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genefu.Rcheck |
| Warnings: 6 |
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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:genefu.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings genefu_2.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/genefu.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 'genefu/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genefu' version '2.14.0'
* 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'
NOTE
Depends: includes the non-default packages:
'survcomp' 'mclust' 'limma' 'biomaRt' 'iC10' 'AIMS'
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 'genefu' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/expos.Rd:23: file link 'data.expos' in package 'genefu' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/nkis.Rd:23: file link 'data.nkis' in package 'genefu' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/read.m.file.Rd:16: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/vdxs.Rd:23: file link 'data.vdxs' in package 'genefu' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/write.m.file.Rd:22: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/genefu.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 6.6Mb
sub-directories of 1Mb or more:
data 5.0Mb
* 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 ... WARNING
'library' or 'require' call not declared from: 'impute'
'library' or 'require' call to 'impute' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'limma'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
'mclust:::grid1' 'mclust:::grid2'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... WARNING
compare:
function(obj, iC10, newdata, name.test, ...)
compare.proto.cor:
function(gene.cor, proto.cor, nn, p.adjust.m)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.ovcSigs: no visible global function definition for 'read.csv'
bimod: no visible global function definition for 'complete.cases'
boxplotplus2: no visible global function definition for 'boxplot'
boxplotplus2: no visible global function definition for 'points'
claudinLow: no visible global function definition for 'standardize'
claudinLow: no visible binding for global variable 'bwss'
claudinLow: no visible global function definition for 'dist'
claudinLow: no visible global function definition for 'cor'
collapseIDs: no visible binding for global variable 'median'
collapseIDs: no visible binding for global variable 'sd'
collapseIDs : <anonymous>: no visible global function definition for
'quantile'
compare.proto.cor: no visible global function definition for 'p.adjust'
compute.pairw.cor.meta: no visible global function definition for 'cor'
compute.pairw.cor.meta: no visible global function definition for
'complete.cases'
compute.pairw.cor.z: no visible global function definition for 'cor'
compute.pairw.cor.z: no visible global function definition for
'complete.cases'
compute.proto.cor.meta : <anonymous>: no visible global function
definition for 'complete.cases'
compute.proto.cor.meta : <anonymous>: no visible global function
definition for 'cor'
compute.proto.cor.meta: no visible global function definition for
'complete.cases'
compute.proto.cor.meta: no visible global function definition for 'cor'
cordiff.dep: no visible global function definition for 'pt'
endoPredict : <anonymous>: no visible global function definition for
'quantile'
fuzzy.ttest: no visible global function definition for 'complete.cases'
fuzzy.ttest: no visible global function definition for 'pt'
gene70 : <anonymous>: no visible global function definition for
'complete.cases'
gene70 : <anonymous>: no visible global function definition for 'cor'
geneid.map: no visible binding for global variable 'sd'
ihc4: no visible global function definition for 'complete.cases'
intrinsic.cluster: no visible global function definition for 'cutree'
intrinsic.cluster: no visible binding for global variable 'median'
intrinsic.cluster : <anonymous>: no visible global function definition
for 'cor'
intrinsic.cluster: no visible global function definition for
'write.table'
intrinsic.cluster.predict: no visible global function definition for
'read.csv'
intrinsic.cluster.predict : <anonymous>: no visible global function
definition for 'complete.cases'
intrinsic.cluster.predict : <anonymous>: no visible global function
definition for 'cor'
intrinsic.cluster.predict: no visible global function definition for
'cutree'
intrinsic.cluster.predict: no visible binding for global variable
'median'
medianCtr: no visible binding for global variable 'median'
molecular.subtyping: no visible binding for global variable 'gt'
molecular.subtyping: no visible binding for global variable 'verbose'
molecular.subtyping : <anonymous>: no visible global function
definition for 'complete.cases'
molecular.subtyping : <anonymous>: no visible global function
definition for 'cor'
molecular.subtyping: no visible binding for global variable
'method.cor'
npi: no visible global function definition for 'complete.cases'
oncotypedx: no visible global function definition for 'complete.cases'
ovcCrijns: no visible global function definition for 'median'
ovcTCGA : <anonymous>: no visible global function definition for
't.test'
ovcYoshihara: no visible global function definition for 'median'
power.cor: no visible global function definition for 'qnorm'
ps.cluster: no visible global function definition for 'complete.cases'
read.m.file: no visible global function definition for 'read.csv'
readarray: no visible global function definition for 'read.table'
readarray: no visible global function definition for 'impute.knn'
rescale: no visible global function definition for 'quantile'
rorS: no visible global function definition for 'quantile'
spearmanCI: no visible global function definition for 'qnorm'
spearmanCI: no visible global function definition for 'pnorm'
st.gallen: no visible global function definition for 'complete.cases'
subtype.cluster: no visible global function definition for
'complete.cases'
subtype.cluster: no visible global function definition for 'median'
subtype.cluster: no visible global function definition for 'par'
subtype.cluster: no visible global function definition for 'persp'
subtype.cluster: no visible global function definition for 'pnorm'
subtype.cluster: no visible global function definition for 'legend'
subtype.cluster.predict: no visible global function definition for
'complete.cases'
subtype.cluster.predict: no visible global function definition for
'median'
subtype.cluster.predict: no visible global function definition for
'pnorm'
subtype.cluster.predict: no visible global function definition for
'legend'
tbrm: no visible global function definition for 'median'
weighted.meanvar: no visible global function definition for
'complete.cases'
write.m.file: no visible global function definition for 'write.table'
Undefined global functions or variables:
boxplot bwss complete.cases cor cutree dist gt impute.knn legend
median method.cor p.adjust par persp pnorm points pt qnorm quantile
read.csv read.table sd standardize t.test verbose write.table
Consider adding
importFrom("graphics", "boxplot", "legend", "par", "persp", "points")
importFrom("stats", "complete.cases", "cor", "cutree", "dist",
"median", "p.adjust", "pnorm", "pt", "qnorm", "quantile",
"sd", "t.test")
importFrom("utils", "read.csv", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Unknown packages 'claudinLow', 'multilevel', 'dplR' in Rd xrefs
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'readarray'
All user-level objects in a package 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 ... WARNING
Bad \usage lines found in documentation object 'collapseIDs':
collapseIDs<-(x,allids=row.names(x),method="mean")
Bad \usage lines found in documentation object 'readArray':
readarray<-function(dataFile,designFile=NA,hr=1,impute=T,method="mean")
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'compare.proto.cor':
'compare.proto.cor'
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: 6 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/genefu.Rcheck/00check.log'
for details.
genefu.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/genefu_2.14.0.tar.gz && rm -rf genefu.buildbin-libdir && mkdir genefu.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genefu.buildbin-libdir genefu_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL genefu_2.14.0.zip && rm genefu_2.14.0.tar.gz genefu_2.14.0.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 4324k 100 4324k 0 0 10.2M 0 --:--:-- --:--:-- --:--:-- 10.3M
install for i386
* installing *source* package 'genefu' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'genefu'
finding HTML links ... done
bimod html
boxplotplus2 html
claudinLow html
claudinLowData html
collapseIDs html
compare.proto.cor html
compute.pairw.cor.meta html
compute.pairw.cor.z html
compute.proto.cor.meta html
cordiff.dep html
endoPredict html
expos html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/expos.Rd:23: file link 'data.expos' in package 'genefu' does not exist and so has been treated as a topic
fuzzy.ttest html
gene70 html
gene76 html
genefu-package html
geneid.map html
genius html
ggi html
ihc4 html
intrinsic.cluster html
intrinsic.cluster.predict html
map.datasets html
medianCtr html
mod1 html
mod2 html
modelOvcAngiogenic html
molecular.subtyping html
nkis html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/nkis.Rd:23: file link 'data.nkis' in package 'genefu' does not exist and so has been treated as a topic
npi html
oncotypedx html
ovcAngiogenic html
ovcCrijns html
ovcTCGA html
ovcYoshihara html
overlapSets html
pam50 html
pik3cags html
power.cor html
ps.cluster html
read.m.file html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/read.m.file.Rd:16: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
readArray html
rename.duplicate html
rescale html
rorS html
scmgene.robust html
scmod1.robust html
scmod2.robust html
setcolclass.df html
sig.endoPredict html
sig.gene70 html
sig.gene76 html
sig.genius html
sig.ggi html
sig.oncotypedx html
sig.pik3cags html
sig.score html
sig.tamr13 html
sigOvcAngiogenic html
sigOvcCrijns html
sigOvcSpentzos html
sigOvcTCGA html
sigOvcYoshihara html
spearmanCI html
ssp2003 html
ssp2006 html
st.gallen html
stab.fs html
stab.fs.ranking html
strescR html
subtype.cluster html
subtype.cluster.predict html
tamr13 html
tbrm html
vdxs html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/vdxs.Rd:23: file link 'data.vdxs' in package 'genefu' does not exist and so has been treated as a topic
weighted.meanvar html
write.m.file html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaw6DtE/R.INSTALL16046deb7dd8/genefu/man/write.m.file.Rd:22: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'genefu' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genefu' as genefu_2.14.0.zip
* DONE (genefu)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'genefu' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
genefu.Rcheck/examples_i386/genefu-Ex.timings
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genefu.Rcheck/examples_x64/genefu-Ex.timings
|