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CHECK report for gaga on machv2

This page was generated on 2020-10-17 11:58:31 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE gaga PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 648/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaga 2.34.0
David Rossell
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/gaga
Branch: RELEASE_3_11
Last Commit: 014dd85
Last Changed Date: 2020-04-27 14:16:16 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: gaga
Version: 2.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gaga.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gaga_2.34.0.tar.gz
StartedAt: 2020-10-17 01:17:47 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:19:15 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 88.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: gaga.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gaga.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gaga_2.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/gaga.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gaga/DESCRIPTION’ ... OK
* this is package ‘gaga’ version ‘2.34.0’
* 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 ‘gaga’ can be installed ... WARNING
Found the following significant warnings:
  cstat.c:1838:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/gaga.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
adjustfitNN: no visible global function definition for ‘predict’
checkfit.gagafit: no visible global function definition for ‘is’
checkfit.gagafit: no visible global function definition for ‘density’
checkfit.gagafit: no visible global function definition for ‘lines’
checkfit.gagafit: no visible global function definition for ‘legend’
checkfit.gagafit: no visible global function definition for ‘quantile’
checkfit.gagafit: no visible global function definition for ‘points’
classpred.gagafit: no visible global function definition for ‘is’
findgenes.gagafit: no visible global function definition for ‘is’
findgenes.gagafit: no visible global function definition for ‘kmeans’
fitGG: no visible global function definition for ‘is’
fitGG: no visible global function definition for ‘quantile’
fitGG: no visible global function definition for ‘var’
fitGG: no visible global function definition for ‘kmeans’
fitNN: no visible global function definition for ‘is’
fitNNSingleHyp: no visible global function definition for ‘is’
forwsimDiffExpr.gagafit: no visible global function definition for ‘is’
forwsimDiffExpr.nnfit: no visible global function definition for ‘is’
forwsimDiffExpr.nnfit: no visible global function definition for
  ‘quantile’
makeEBarraysSingleHyp: no visible global function definition for ‘new’
parest.gagafit: no visible global function definition for ‘is’
parest.gagafit: no visible binding for global variable ‘quantile’
parest.gagafit: no visible global function definition for ‘quantile’
plotForwSim: no visible global function definition for ‘lines’
posmeansGG.gagafit: no visible global function definition for ‘is’
powclasspred.gagafit: no visible global function definition for ‘is’
powfindgenes.gagafit: no visible global function definition for ‘is’
powfindgenes.nnfit: no visible global function definition for ‘is’
powfindgenes.nnfit: no visible global function definition for ‘sd’
powsimprior.nnfit: no visible global function definition for ‘sd’
ppGG: no visible global function definition for ‘is’
sigmaPriorEst: no visible global function definition for ‘is’
sigmaPriorEst: no visible binding for global variable ‘var’
sigmaPriorEst: no visible global function definition for ‘var’
simGG: no visible global function definition for ‘rgamma’
simGG: no visible global function definition for ‘new’
simNN: no visible global function definition for ‘runif’
simNN: no visible global function definition for ‘rnorm’
simNN: no visible global function definition for ‘rgamma’
simNN: no visible global function definition for ‘new’
simnewsamples.gagafit: no visible global function definition for ‘is’
simnewsamples.gagafit: no visible global function definition for ‘new’
simnewsamples.nnfit: no visible global function definition for ‘is’
simnewsamples.nnfit: no visible global function definition for ‘runif’
simnewsamples.nnfit: no visible global function definition for ‘rgamma’
simnewsamples.nnfit: no visible global function definition for ‘rnorm’
simnewsamples.nnfit: no visible global function definition for
  ‘model.matrix’
simnewsamples.nnfit: no visible global function definition for ‘new’
Undefined global functions or variables:
  density is kmeans legend lines model.matrix new points predict
  quantile rgamma rnorm runif sd var
Consider adding
  importFrom("graphics", "legend", "lines", "points")
  importFrom("methods", "is", "new")
  importFrom("stats", "density", "kmeans", "model.matrix", "predict",
             "quantile", "rgamma", "rnorm", "runif", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/gaga.Rcheck/00check.log’
for details.



Installation output

gaga.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gaga
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘gaga’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cseqdesma.c -o cseqdesma.o
cseqdesma.c:4524:14: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((*usesumx==0)) {                                               //if suff stat not pre-computed
     ~~~~~~~~^~~
cseqdesma.c:4524:14: note: remove extraneous parentheses around the comparison to silence this warning
if ((*usesumx==0)) {                                               //if suff stat not pre-computed
    ~        ^  ~
cseqdesma.c:4524:14: note: use '=' to turn this equality comparison into an assignment
if ((*usesumx==0)) {                                               //if suff stat not pre-computed
             ^~
             =
cseqdesma.c:5836:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
  if ((*usel==0)) {
       ~~~~~^~~
cseqdesma.c:5836:13: note: remove extraneous parentheses around the comparison to silence this warning
  if ((*usel==0)) {
      ~     ^  ~
cseqdesma.c:5836:13: note: use '=' to turn this equality comparison into an assignment
  if ((*usel==0)) {
            ^~
            =
cseqdesma.c:6070:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
  if ((*usel==0)) {
       ~~~~~^~~
cseqdesma.c:6070:13: note: remove extraneous parentheses around the comparison to silence this warning
  if ((*usel==0)) {
      ~     ^  ~
cseqdesma.c:6070:13: note: use '=' to turn this equality comparison into an assignment
  if ((*usel==0)) {
            ^~
            =
cseqdesma.c:6340:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
  if ((*usel==0)) {                                           //If l values have to be generated
       ~~~~~^~~
cseqdesma.c:6340:13: note: remove extraneous parentheses around the comparison to silence this warning
  if ((*usel==0)) {                                           //If l values have to be generated
      ~     ^  ~
cseqdesma.c:6340:13: note: use '=' to turn this equality comparison into an assignment
  if ((*usel==0)) {                                           //If l values have to be generated
            ^~
            =
4 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cstat.c -o cstat.o
cstat.c:1838:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  if(abs(ndf - 2.0) < eps) {   /* df ~= 2 */
     ^
cstat.c:1838:6: note: use function 'fabs' instead
  if(abs(ndf - 2.0) < eps) {   /* df ~= 2 */
     ^~~
     fabs
cstat.c:18:19: warning: unused variable 'interface_c_sccs_id' [-Wunused-const-variable]
static const char interface_c_sccs_id[] = "%W%";
                  ^
cstat.c:19:19: warning: unused variable 'mess_c_sccs_id' [-Wunused-const-variable]
static const char mess_c_sccs_id[] = "%W%";
                  ^
cstat.c:20:19: warning: unused variable 'nrutil_c_sccs_id' [-Wunused-const-variable]
static const char nrutil_c_sccs_id[] = "%W%"; 
                  ^
cstat.c:21:19: warning: unused variable 'vector_c_sccs_id' [-Wunused-const-variable]
static const char vector_c_sccs_id[] = "%W%";
                  ^
cstat.c:22:19: warning: unused variable 'css_c_sccs_id' [-Wunused-const-variable]
static const char css_c_sccs_id[] = "@(#)$Workfile: rand.c$ $Revision: 5$";
                  ^
6 warnings generated.
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o gaga.so cseqdesma.o cstat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-gaga/00new/gaga/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gaga)

Tests output


Example timings

gaga.Rcheck/gaga-Ex.timings

nameusersystemelapsed
buildPatterns0.0290.0010.031
classpred0.0000.0010.001
findgenes0.0000.0010.000
fitGG0.1910.0040.198
forwsimDiffExpr1.7340.0061.743
geneclus0.0010.0000.001
parest0.0000.0000.001
powfindgenes0.3330.0020.335
simGG0.0000.0000.001