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BioC 3.4: CHECK report for nethet on tokay1

This page was generated on 2017-04-15 16:19:27 -0400 (Sat, 15 Apr 2017).

Package 836/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nethet 1.6.0
Nicolas Staedler
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/nethet
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: nethet
Version: 1.6.0
Command: rm -rf nethet.buildbin-libdir nethet.Rcheck && mkdir nethet.buildbin-libdir nethet.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=nethet.buildbin-libdir nethet_1.6.0.tar.gz >nethet.Rcheck\00install.out 2>&1 && cp nethet.Rcheck\00install.out nethet-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=nethet.buildbin-libdir --install="check:nethet-install.out" --force-multiarch --no-vignettes --timings nethet_1.6.0.tar.gz
StartedAt: 2017-04-14 23:48:27 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:53:31 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 304.1 seconds
RetCode: 0
Status:  OK  
CheckDir: nethet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf nethet.buildbin-libdir nethet.Rcheck && mkdir nethet.buildbin-libdir nethet.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=nethet.buildbin-libdir nethet_1.6.0.tar.gz >nethet.Rcheck\00install.out 2>&1 && cp nethet.Rcheck\00install.out nethet-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=nethet.buildbin-libdir --install="check:nethet-install.out" --force-multiarch --no-vignettes --timings nethet_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/nethet.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.6.0'
* 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 ... 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
* 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
** checking loading without being on the library search path ... 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 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 ... 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-3.4-bioc/meat/nethet.buildbin-libdir/nethet/libs/i386/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 the system RNG.
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 installed files from 'inst/doc' ... OK
* 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       22.78   0.00   22.80
mixglasso           16.69   0.03   16.72
ggmgsa_multisplit   13.61   0.00   13.61
diffregr_multisplit  7.71   0.02    7.73
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
het_cv_glasso       34.45   0.00   34.45
ggmgsa_multisplit   21.92   0.02   21.97
mixglasso           16.98   0.00   16.98
diffregr_multisplit  8.32   0.01    8.33
diffnet_multisplit   5.76   0.00    5.89
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/nethet.Rcheck/00check.log'
for details.


nethet.Rcheck/00install.out:


install for i386

* installing *source* package 'nethet' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/nethet.buildbin-libdir/nethet/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'nethet' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/nethet.buildbin-libdir/nethet/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nethet' as nethet_1.6.0.zip
* DONE (nethet)

nethet.Rcheck/examples_i386/nethet-Ex.timings:

nameusersystemelapsed
aggpval000
bwprun_mixglasso4.180.014.21
diffnet_multisplit4.410.004.61
diffnet_singlesplit2.080.002.08
diffregr_multisplit7.710.027.73
diffregr_singlesplit0.580.000.57
dot_plot0.710.000.72
export_network0.290.000.28
generate_2networks0.060.000.07
generate_inv_cov0.080.030.11
ggmgsa_multisplit13.61 0.0013.61
gsea.iriz000
het_cv_glasso22.78 0.0022.80
invcov2parcor000
invcov2parcor_array000
logratio000
mixglasso16.69 0.0316.72
plot_2networks0.060.020.08
scatter_plot1.840.051.89
screen_aic.glasso0.610.000.61
screen_bic.glasso0.630.000.63
screen_cv.glasso1.50.01.5
screen_cv1se.lasso0.170.000.17
screen_cvfix.lasso0.120.000.12
screen_cvmin.lasso0.160.000.16
screen_cvsqrt.lasso0.140.000.14
screen_cvtrunc.lasso0.20.00.2
screen_mb0.020.000.02
sim_mix000
sim_mix_networks000

nethet.Rcheck/examples_x64/nethet-Ex.timings:

nameusersystemelapsed
aggpval000
bwprun_mixglasso3.110.043.19
diffnet_multisplit5.760.005.89
diffnet_singlesplit2.760.002.77
diffregr_multisplit8.320.018.33
diffregr_singlesplit0.620.000.62
dot_plot0.780.020.80
export_network0.270.000.26
generate_2networks0.250.000.25
generate_inv_cov0.060.040.11
ggmgsa_multisplit21.92 0.0221.97
gsea.iriz0.020.000.02
het_cv_glasso34.45 0.0034.45
invcov2parcor000
invcov2parcor_array000
logratio0.020.000.02
mixglasso16.98 0.0016.98
plot_2networks0.060.000.06
scatter_plot1.690.021.71
screen_aic.glasso0.940.000.93
screen_bic.glasso0.790.000.80
screen_cv.glasso1.930.001.92
screen_cv1se.lasso0.150.000.16
screen_cvfix.lasso0.160.000.15
screen_cvmin.lasso0.140.000.15
screen_cvsqrt.lasso0.160.000.15
screen_cvtrunc.lasso0.150.000.16
screen_mb000
sim_mix000
sim_mix_networks0.020.000.01