Nicolas Staedler
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/nethet |
| Branch: RELEASE_3_12 |
| Last Commit: 09eb075 |
| Last Changed Date: 2020-10-27 11:01:24 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:27 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the nethet package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1217/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nethet 1.22.0 (landing page) Nicolas Staedler
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: nethet |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nethet.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings nethet_1.22.0.tar.gz |
| StartedAt: 2021-05-06 05:04:36 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:10:05 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 329.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: nethet.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nethet.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings nethet_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/nethet.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.22.0'
* 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 'nethet' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
Warning: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet'
See 'C:/Users/biocbuild/bbs-3.12-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
screen_shrink: no visible global function definition for
'performance.pcor'
Undefined global functions or variables:
performance.pcor
* 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-3.12-bioc/R/library/nethet/libs/i386/nethet.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-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 (user + system) or elapsed time > 5s
user system elapsed
het_cv_glasso 33.83 0.00 33.88
ggmgsa_multisplit 17.75 0.00 17.75
mixglasso 15.68 0.11 16.32
diffregr_multisplit 8.48 0.10 8.58
diffnet_multisplit 5.06 0.00 6.27
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
het_cv_glasso 34.00 0.00 34.00
ggmgsa_multisplit 22.06 0.00 22.06
mixglasso 11.21 0.09 11.31
diffregr_multisplit 8.29 0.03 8.31
diffnet_multisplit 5.60 0.00 5.94
* 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-3.12-bioc/meat/nethet.Rcheck/00check.log'
for details.
nethet.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/nethet_1.22.0.tar.gz && rm -rf nethet.buildbin-libdir && mkdir nethet.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nethet.buildbin-libdir nethet_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL nethet_1.22.0.zip && rm nethet_1.22.0.tar.gz nethet_1.22.0.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 90144 100 90144 0 0 323k 0 --:--:-- --:--:-- --:--:-- 324k
install for i386
* installing *source* package 'nethet' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c betamat_diffnet.c -o betamat_diffnet.o
C:/rtools40/mingw32/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-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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'
Warning: replacing previous import 'multtest::update' by 'stats::update' 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_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'
Warning: replacing previous import 'multtest::update' by 'stats::update' 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'
Warning: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'nethet' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c betamat_diffnet.c -o betamat_diffnet.o
C:/rtools40/mingw64/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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-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'
Warning: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet'
* MD5 sums
packaged installation of 'nethet' as nethet_1.22.0.zip
* DONE (nethet)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'nethet' successfully unpacked and MD5 sums checked
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nethet.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 messages:
1: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
2: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet'
>
> test_check("nethet")
-mixglasso: comp too small; min(n_k)= 4.051777
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
>
> proc.time()
user system elapsed
6.89 0.32 7.20
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nethet.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 messages:
1: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
2: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet'
>
> test_check("nethet")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
>
> proc.time()
user system elapsed
8.71 0.35 9.06
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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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