Nicolas Staedler
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/nethet |
| git_branch: master |
| git_last_commit: ae9cf28 |
| git_last_commit_date: 2021-10-26 12:18:03 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:10 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the nethet package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/nethet.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1291/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nethet 1.27.0 (landing page) Nicolas Staedler
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: nethet |
| Version: 1.27.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nethet.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings nethet_1.27.0.tar.gz |
| StartedAt: 2022-03-17 19:43:40 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:46:27 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 167.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: nethet.Rcheck |
| Warnings: 1 |
##############################################################################
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nethet.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings nethet_1.27.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/nethet.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.27.0'
* 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 'D:/biocbuild/bbs-3.15-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
* 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 x64 is not available
File 'D:/biocbuild/bbs-3.15-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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
het_cv_glasso 23.38 0.03 23.41
ggmgsa_multisplit 15.47 0.00 15.47
mixglasso 10.04 0.26 10.32
diffregr_multisplit 6.12 0.26 6.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
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
'D:/biocbuild/bbs-3.15-bioc/meat/nethet.Rcheck/00check.log'
for details.
nethet.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL nethet
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'nethet' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-nethet/00new/nethet/libs/x64
** 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
* DONE (nethet)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'qcmetrics' is missing or broken
done
nethet.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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")
-mixglasso: comp too small; min(n_k)= 4.311776
-mixglasso: comp too small; min(n_k)= 4.625246
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
>
> proc.time()
user system elapsed
4.79 0.37 5.21
nethet.Rcheck/nethet-Ex.timings
| name | user | system | elapsed | |
| aggpval | 0 | 0 | 0 | |
| bwprun_mixglasso | 1.69 | 0.25 | 1.94 | |
| diffnet_multisplit | 4.54 | 0.00 | 4.55 | |
| diffnet_singlesplit | 2.08 | 0.00 | 2.08 | |
| diffregr_multisplit | 6.12 | 0.26 | 6.39 | |
| diffregr_singlesplit | 0.55 | 0.00 | 0.55 | |
| dot_plot | 0.59 | 0.07 | 0.65 | |
| export_network | 0.10 | 0.01 | 0.11 | |
| generate_2networks | 0.03 | 0.00 | 0.03 | |
| generate_inv_cov | 0.06 | 0.05 | 0.11 | |
| ggmgsa_multisplit | 15.47 | 0.00 | 15.47 | |
| gsea.iriz | 0 | 0 | 0 | |
| het_cv_glasso | 23.38 | 0.03 | 23.41 | |
| invcov2parcor | 0 | 0 | 0 | |
| invcov2parcor_array | 0.00 | 0.02 | 0.01 | |
| logratio | 0 | 0 | 0 | |
| mixglasso | 10.04 | 0.26 | 10.32 | |
| plot_2networks | 0.05 | 0.00 | 0.04 | |
| scatter_plot | 1.34 | 0.00 | 1.35 | |
| screen_aic.glasso | 0.85 | 0.00 | 0.84 | |
| screen_bic.glasso | 0.83 | 0.00 | 0.82 | |
| screen_cv.glasso | 1.56 | 0.00 | 1.57 | |
| screen_cv1se.lasso | 0.16 | 0.00 | 0.15 | |
| screen_cvfix.lasso | 0.09 | 0.00 | 0.10 | |
| screen_cvmin.lasso | 0.11 | 0.00 | 0.11 | |
| screen_cvsqrt.lasso | 0.10 | 0.00 | 0.09 | |
| screen_cvtrunc.lasso | 0.09 | 0.00 | 0.09 | |
| sim_mix | 0 | 0 | 0 | |
| sim_mix_networks | 0 | 0 | 0 | |