Nicolas Staedler
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/nethet |
| Branch: RELEASE_3_9 |
| Last Commit: da529d3 |
| Last Changed Date: 2019-06-20 11:15:59 -0400 (Thu, 20 Jun 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:32:03 -0400 (Wed, 16 Oct 2019).
| Package 1096/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| nethet 1.16.1 Nicolas Staedler
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: nethet |
| Version: 1.16.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nethet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings nethet_1.16.1.tar.gz |
| StartedAt: 2019-10-16 05:35:11 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:40:41 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 329.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: nethet.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nethet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings nethet_1.16.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/nethet.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 'nethet/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'nethet' version '1.16.1' * 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 'nethet' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet' See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/nethet.Rcheck/00install.out' for details. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE MStepGlasso: no visible global function definition for 'cov.wt' agg.pval: no visible global function definition for 'quantile' aggpval: no visible global function definition for 'optimize' aggpval :: no visible global function definition for 'quantile' aic.glasso: no visible global function definition for 'var' bic.glasso: no visible global function definition for 'var' cv.glasso: no visible global function definition for 'var' cv.glasso: no visible binding for global variable 'var' diffnet_multisplit: no visible global function definition for 'optimize' diffnet_multisplit: no visible binding for global variable 'median' diffnet_multisplit: no visible global function definition for 'median' diffregr_multisplit: no visible global function definition for 'optimize' diffregr_multisplit: no visible global function definition for 'median' diffregr_singlesplit: no visible global function definition for 'coef' diffregr_singlesplit: no visible global function definition for 'lm' error.bars: no visible global function definition for 'segments' est2.my.ev2.diffregr: no visible global function definition for 'var' est2.my.ev3.diffregr: no visible global function definition for 'var' est2.ww.mat.diffregr: no visible global function definition for 'var' est2.ww.mat2.diffregr: no visible global function definition for 'var' export_network: no visible global function definition for 'write.csv' func.uinit: no visible global function definition for 'kmeans' getinvcov: no visible global function definition for 'rbeta' ggmgsa_multisplit: no visible binding for global variable 'median' glasso.parcor: no visible global function definition for 'sd' gsea.iriz.scale: no visible global function definition for 'pnorm' gsea.iriz.shift: no visible global function definition for 'pnorm' lambda.max: no visible global function definition for 'var' logratio.diffregr: no visible global function definition for 'dnorm' mcov: no visible global function definition for 'cov.wt' mcov: no visible global function definition for 'var' mixglasso_init: no visible global function definition for 'cov.wt' my.p.adjust: no visible global function definition for 'p.adjust' my.ttest: no visible global function definition for 'var' my.ttest2: no visible global function definition for 'var' perm.diffregr_teststat: no visible global function definition for 'coef' perm.diffregr_teststat: no visible global function definition for 'lm' plot.diffnet: no visible global function definition for 'hist' plot.diffnet: no visible global function definition for 'abline' plot.diffnet: no visible global function definition for 'legend' plot.diffregr: no visible global function definition for 'hist' plot.diffregr: no visible global function definition for 'abline' plot.diffregr: no visible global function definition for 'legend' plot.ggmgsa: no visible global function definition for 'boxplot' plot.nethetclustering: no visible global function definition for 'pdf' plot.nethetclustering: no visible global function definition for 'grey' plot.nethetclustering: no visible global function definition for 'legend' plot.nethetclustering: no visible global function definition for 'dev.off' plot_2networks: no visible global function definition for 'par' scatter_plot : : no visible global function definition for 'cor' screen_cv.glasso: no visible global function definition for 'var' screen_cv.glasso: no visible binding for global variable 'var' screen_cv1se.lasso: no visible global function definition for 'coef' screen_cvfix.lasso: no visible global function definition for 'coef' screen_cvmin.lasso: no visible global function definition for 'coef' screen_cvsqrt.lasso: no visible global function definition for 'coef' screen_cvtrunc.lasso: no visible global function definition for 'coef' screen_mb: no visible global function definition for 'var' screen_mb: no visible binding for global variable 'var' screen_mb2 : : no visible global function definition for 'lines' screen_mb2 : : no visible global function definition for 'coef' shapiro_screen : : no visible global function definition for 'shapiro.test' shapiro_screen: no visible global function definition for 'p.adjust' sim_mix_networks : : no visible global function definition for 'rnorm' t2cov.lr: no visible global function definition for 'var' t2cov.lr: no visible global function definition for 'pchisq' t2diagcov.lr: no visible global function definition for 'var' t2diagcov.lr: no visible global function definition for 'pchisq' test.sd: no visible global function definition for 'var' test.sd: no visible global function definition for 'pnorm' twosample_single_regr: no visible global function definition for 'coef' twosample_single_regr: no visible global function definition for 'lm' Undefined global functions or variables: abline boxplot coef cor cov.wt dev.off dnorm grey hist kmeans legend lines lm median optimize p.adjust par pchisq pdf pnorm quantile rbeta rnorm sd segments shapiro.test var write.csv Consider adding importFrom("grDevices", "dev.off", "grey", "pdf") importFrom("graphics", "abline", "boxplot", "hist", "legend", "lines", "par", "segments") importFrom("stats", "coef", "cor", "cov.wt", "dnorm", "kmeans", "lm", "median", "optimize", "p.adjust", "pchisq", "pnorm", "quantile", "rbeta", "rnorm", "sd", "shapiro.test", "var") importFrom("utils", "write.csv") 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/nethet/libs/i386/nethet.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/nethet/libs/x64/nethet.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed het_cv_glasso 30.30 0.00 30.30 ggmgsa_multisplit 15.81 0.00 15.81 mixglasso 14.56 0.11 14.67 diffregr_multisplit 7.50 0.06 7.56 diffnet_multisplit 5.35 0.00 5.63 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed het_cv_glasso 28.89 0.00 28.89 ggmgsa_multisplit 16.98 0.00 16.99 mixglasso 14.17 0.02 14.19 diffregr_multisplit 7.40 0.05 7.46 diffnet_multisplit 5.35 0.00 5.52 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' 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, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/nethet.Rcheck/00check.log' for details.
nethet.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/nethet_1.16.1.tar.gz && rm -rf nethet.buildbin-libdir && mkdir nethet.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nethet.buildbin-libdir nethet_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL nethet_1.16.1.zip && rm nethet_1.16.1.tar.gz nethet_1.16.1.zip
###
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install for i386
* installing *source* package 'nethet' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c betamat_diffnet.c -o betamat_diffnet.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o nethet.dll tmp.def betamat_diffnet.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/nethet.buildbin-libdir/00LOCK-nethet/00new/nethet/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
** help
*** installing help indices
converting help for package 'nethet'
finding HTML links ... done
EXPStep.mix html
MStepGlasso html
NetHet-package html
agg.pval html
agg.score.iriz.scale html
agg.score.iriz.shift html
aggpval html
aic.glasso html
beta.mat html
beta.mat.diffregr html
bic.glasso html
buildDotPlotDataFrame html
bwprun_mixglasso html
cv.fold html
cv.glasso html
diffnet_multisplit html
diffnet_pval html
diffnet_singlesplit html
diffregr_multisplit html
diffregr_pval html
diffregr_singlesplit html
dot_plot html
error.bars html
est2.my.ev2 html
est2.my.ev2.diffregr html
est2.my.ev3 html
est2.my.ev3.diffregr html
est2.ww.mat.diffregr html
est2.ww.mat2 html
est2.ww.mat2.diffregr html
export_network html
func.uinit html
generate_2networks html
generate_inv_cov html
getinvcov html
ggmgsa_multisplit html
ggmgsa_singlesplit html
glasso.invcor html
glasso.invcov html
glasso.parcor html
gsea.highdimT2 html
gsea.iriz html
gsea.iriz.scale html
gsea.iriz.shift html
gsea.t2cov html
het_cv_glasso html
hugepath html
inf.mat html
invcov2parcor html
invcov2parcor_array html
lambda.max html
lambdagrid_lin html
lambdagrid_mult html
loglik_mix html
logratio html
logratio.diffregr html
make_grid html
mcov html
mixglasso html
mixglasso_init html
mixglasso_ncomp_fixed html
mle.ggm html
my.ev2.diffregr html
my.p.adjust html
my.ttest html
my.ttest2 html
mytrunc.method html
perm.diffregr_pval html
perm.diffregr_teststat html
plot.diffnet html
plot.diffregr html
plot.ggmgsa html
plot.nethetclustering html
plotCV html
plot_2networks html
print.nethetsummary html
q.matrix.diffregr html
q.matrix.diffregr3 html
q.matrix.diffregr4 html
q.matrix3 html
q.matrix4 html
scatter_plot html
screen_aic.glasso html
screen_bic.glasso html
screen_cv.glasso html
screen_cv1se.lasso html
screen_cvfix.lasso html
screen_cvmin.lasso html
screen_cvsqrt.lasso html
screen_cvtrunc.lasso html
screen_full html
screen_lasso html
screen_mb html
screen_mb2 html
screen_shrink html
shapiro_screen html
sim_mix html
sim_mix_networks html
sparse_conc html
summary.diffnet html
summary.diffregr html
summary.ggmgsa html
summary.nethetclustering html
sumoffdiag html
symmkldist html
t2cov.lr html
t2diagcov.lr html
test.sd html
test.t2 html
tr html
twosample_single_regr html
w.kldist html
ww.mat html
ww.mat.diffregr html
ww.mat2 html
ww.mat2.diffregr html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'nethet' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c betamat_diffnet.c -o betamat_diffnet.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o nethet.dll tmp.def betamat_diffnet.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/nethet.buildbin-libdir/nethet/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
* MD5 sums
packaged installation of 'nethet' as nethet_1.16.1.zip
* DONE (nethet)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'nethet' successfully unpacked and MD5 sums checked
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nethet.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(nethet)
Warning message:
replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
>
> test_check("nethet")
== testthat results ===========================================================
[ OK: 18 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
10.25 0.39 10.60
|
nethet.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(nethet)
Warning message:
replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
>
> test_check("nethet")
-mixglasso: comp too small; min(n_k)= 3.664816
-mixglasso: comp too small; min(n_k)= 4.209627
== testthat results ===========================================================
[ OK: 18 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
8.59 0.31 8.87
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nethet.Rcheck/examples_i386/nethet-Ex.timings
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nethet.Rcheck/examples_x64/nethet-Ex.timings
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