Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:13:03 -0400 (Thu, 12 Apr 2018).
Package 936/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
nethet 1.10.0 Nicolas Staedler
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: nethet |
Version: 1.10.0 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings nethet_1.10.0.tar.gz |
StartedAt: 2018-04-12 01:27:33 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 01:30:15 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 162.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: nethet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings nethet_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/nethet.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘nethet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘nethet’ version ‘1.10.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘nethet’ 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 * 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 loading without being on the library search path ... 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 : <anonymous>: 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’ 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 : <anonymous>: 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 : <anonymous>: no visible global function definition for ‘lines’ screen_mb2 : <anonymous>: no visible global function definition for ‘coef’ shapiro_screen : <anonymous>: no visible global function definition for ‘shapiro.test’ shapiro_screen: no visible global function definition for ‘p.adjust’ sim_mix_networks : <anonymous>: 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 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", "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 ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed het_cv_glasso 26.120 0.000 26.155 ggmgsa_multisplit 15.704 0.004 15.718 mixglasso 14.128 0.032 14.173 diffregr_multisplit 8.264 0.000 8.268 diffnet_multisplit 6.412 0.000 6.418 * 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 NOTE See ‘/home/biocbuild/bbs-3.6-bioc/meat/nethet.Rcheck/00check.log’ for details.
nethet.Rcheck/00install.out
* installing *source* package ‘nethet’ ... ** libs gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c betamat_diffnet.c -o betamat_diffnet.o g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o nethet.so betamat_diffnet.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.6-bioc/meat/nethet.Rcheck/nethet/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (nethet)
nethet.Rcheck/nethet-Ex.timings
name | user | system | elapsed | |
aggpval | 0.004 | 0.000 | 0.007 | |
bwprun_mixglasso | 3.320 | 0.016 | 3.340 | |
diffnet_multisplit | 6.412 | 0.000 | 6.418 | |
diffnet_singlesplit | 2.440 | 0.004 | 2.446 | |
diffregr_multisplit | 8.264 | 0.000 | 8.268 | |
diffregr_singlesplit | 0.436 | 0.004 | 0.440 | |
dot_plot | 1.932 | 0.004 | 1.935 | |
export_network | 0.272 | 0.000 | 0.274 | |
generate_2networks | 0.040 | 0.000 | 0.038 | |
generate_inv_cov | 0.048 | 0.032 | 0.079 | |
ggmgsa_multisplit | 15.704 | 0.004 | 15.718 | |
gsea.iriz | 0.044 | 0.000 | 0.046 | |
het_cv_glasso | 26.120 | 0.000 | 26.155 | |
invcov2parcor | 0.004 | 0.000 | 0.001 | |
invcov2parcor_array | 0.004 | 0.000 | 0.004 | |
logratio | 0.000 | 0.000 | 0.001 | |
mixglasso | 14.128 | 0.032 | 14.173 | |
plot_2networks | 0.040 | 0.000 | 0.038 | |
scatter_plot | 1.864 | 0.004 | 1.870 | |
screen_aic.glasso | 0.736 | 0.000 | 0.738 | |
screen_bic.glasso | 0.732 | 0.000 | 0.732 | |
screen_cv.glasso | 1.784 | 0.000 | 1.785 | |
screen_cv1se.lasso | 0.128 | 0.000 | 0.128 | |
screen_cvfix.lasso | 0.136 | 0.000 | 0.134 | |
screen_cvmin.lasso | 0.136 | 0.000 | 0.137 | |
screen_cvsqrt.lasso | 0.128 | 0.000 | 0.126 | |
screen_cvtrunc.lasso | 0.128 | 0.000 | 0.129 | |
screen_mb | 0.032 | 0.000 | 0.029 | |
sim_mix | 0.004 | 0.000 | 0.004 | |
sim_mix_networks | 0.012 | 0.000 | 0.012 | |