Multiple platform build/check report for BioC 3.13 - CHECK results for signatureSearch on tokay2

Package: signatureSearch

Version: 1.6.3

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:signatureSearch.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings signatureSearch_1.6.3.tar.gz

StartedAt: 2021-10-15 05:41:58 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 05:51:36 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 578.2 seconds

RetCode: 0

Status: OK

CheckDir: signatureSearch.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:signatureSearch.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings signatureSearch_1.6.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/signatureSearch.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'signatureSearch/DESCRIPTION' ... OK
* this is package 'signatureSearch' version '1.6.3'
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  inst/extdata/.batchtools.conf.R
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'signatureSearch' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 87.9Mb
  sub-directories of 1Mb or more:
    R        82.8Mb
    extdata   1.5Mb
    libs      2.1Mb
* 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 19 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... 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-3.13-bioc/R/library/signatureSearch/libs/i386/signatureSearch.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/signatureSearch/libs/x64/signatureSearch.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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
runWF        29.01   2.67   37.94
set_readable 19.63   1.39   21.36
dtnetplot     5.78   1.59    7.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
runWF        32.06   1.40   39.21
set_readable 19.94   0.75   21.03
dtnetplot     5.78   1.00    7.15
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/signatureSearch.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/signatureSearch_1.6.3.tar.gz && rm -rf signatureSearch.buildbin-libdir && mkdir signatureSearch.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=signatureSearch.buildbin-libdir signatureSearch_1.6.3.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL signatureSearch_1.6.3.zip && rm signatureSearch_1.6.3.tar.gz signatureSearch_1.6.3.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
 39 4187k   39 1640k    0     0  2032k      0  0:00:02 --:--:--  0:00:02 2032k
100 4187k  100 4187k    0     0  2594k      0  0:00:01  0:00:01 --:--:-- 2596k

install for i386

* installing *source* package 'signatureSearch' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function 'Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)':
fastGSEA.cpp:444:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for (int j = 0; j < S.size(); ++j) {
                         ~~^~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fgsea_init.c -o fgsea_init.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o signatureSearch.dll tmp.def RcppExports.o fastGSEA.o fgsea_init.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/signatureSearch.buildbin-libdir/00LOCK-signatureSearch/00new/signatureSearch/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'signatureSearch'
    finding HTML links ... done
    GCT-object                              html  
    add_pcid                                html  
    append2H5                               html  
    build_custom_db                         html  
    calcGseaStatBatchCpp                    html  
    cellNtestPlot                           html  
    cell_info                               html  
    chembl_moa_list                         html  
    clue_moa_list                           html  
    comp_fea_res                            html  
    create_empty_h5                         html  
    dim-methods                             html  
    drug_cell_ranks                         html  
    drugs-methods                           html  
    drugs10                                 html  
    dsea_GSEA                               html  
    dsea_hyperG                             html  
    dtnetplot                               html  
    enrichGO2                               html  
    enrichKEGG2                             html  
    enrichMOA                               html  
    enrichReactome                          html  
    feaResult-class                         html  
    feaResult                               html  
    gctx2h5                                 html  
    gessResult-class                        html  
    gessResult                              html  
    gess_cmap                               html  
    gess_cor                                html  
    gess_fisher                             html  
    gess_gcmap                              html  
    gess_lincs                              html  
    gess_res_vis                            html  
    getALLEG                                html  
    getDb                                   html  
    getSig                                  html  
    get_targets                             html  
    get_treat_info                          html  
    gmt2h5                                  html  
    gseGO2                                  html  
    gseKEGG2                                html  
    gseReactome                             html  
    head-methods                            html  
    lincs_expr_inst_info                    html  
    lincs_pert_info                         html  
    lincs_sig_info                          html  
    list2df                                 html  
    mabsGO                                  html  
    mabsKEGG                                html  
    mabsReactome                            html  
    matrix2h5                               html  
    moa_conn                                html  
    parse_gctx                              html  
    qSig-class                              html  
    qSig                                    html  
    rand_query_ES                           html  
    read_gmt                                html  
    result-methods                          html  
    runWF                                   html  
    set_readable                            html  
    show-methods                            html  
    signatureSearch-package                 html  
    sim_score_grp                           html  
    tail-methods                            html  
    tarReduce                               html  
    targetList                              html  
    tsea_dup_hyperG                         html  
    tsea_mGSEA                              html  
    tsea_mabs                               html  
    vec_char_redu                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'signatureSearch' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function 'Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)':
fastGSEA.cpp:444:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         for (int j = 0; j < S.size(); ++j) {
                         ~~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fgsea_init.c -o fgsea_init.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o signatureSearch.dll tmp.def RcppExports.o fastGSEA.o fgsea_init.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/signatureSearch.buildbin-libdir/signatureSearch/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'signatureSearch' as signatureSearch_1.6.3.zip
* DONE (signatureSearch)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'signatureSearch' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(signatureSearch)
> # 
> # test_check("signatureSearch")
> 
> proc.time()
   user  system elapsed 
   0.17    0.09    0.25


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(signatureSearch)
> # 
> # test_check("signatureSearch")
> 
> proc.time()
   user  system elapsed 
   0.25    0.07    0.29

name	user	system	elapsed
add_pcid	0.01	0.00	0.02
append2H5	0.05	0.02	0.06
build_custom_db	0.23	0.12	0.35
cellNtestPlot	0.39	0.13	0.58
cell_info	0.08	0.09	0.17
chembl_moa_list	0.02	0.00	0.02
clue_moa_list	0.01	0.00	0.02
comp_fea_res	0.22	0.00	0.21
create_empty_h5	0.03	0.00	0.04
dim-methods	0	0	0
drug_cell_ranks	0	0	0
drugs-methods	0.02	0.00	0.01
drugs10	0	0	0
dsea_GSEA	0.01	0.00	0.02
dsea_hyperG	0.00	0.02	0.01
dtnetplot	5.78	1.59	7.86
enrichGO2	0	0	0
enrichKEGG2	0	0	0
enrichMOA	0.02	0.06	0.08
enrichReactome	0	0	0
feaResult	0.02	0.00	0.01
gctx2h5	0.61	0.16	0.86
gessResult	0	0	0
gess_cmap	0	0	0
gess_cor	0	0	0
gess_fisher	0	0	0
gess_gcmap	0	0	0
gess_lincs	0	0	0
gess_res_vis	0.25	0.00	0.25
getSig	0.42	0.04	0.47
get_targets	2.57	0.16	2.90
get_treat_info	0.03	0.00	0.03
gmt2h5	0.11	0.05	0.38
gseGO2	0.00	0.01	0.01
gseKEGG2	0.01	0.00	0.02
gseReactome	0.02	0.00	0.02
head-methods	0.01	0.00	0.01
lincs_expr_inst_info	0.05	0.00	0.05
lincs_pert_info	0.14	0.02	0.15
lincs_sig_info	0.05	0.01	0.07
list2df	0	0	0
mabsGO	0.00	0.02	0.01
mabsKEGG	0.01	0.00	0.02
mabsReactome	0.02	0.00	0.01
matrix2h5	0.08	0.00	0.08
moa_conn	0.03	0.01	0.05
parse_gctx	0.11	0.04	0.14
qSig	0.42	0.01	0.44
rand_query_ES	3.28	0.16	3.50
read_gmt	0	0	0
result-methods	0.02	0.00	0.01
runWF	29.01	2.67	37.94
set_readable	19.63	1.39	21.36
show-methods	0.03	0.00	0.03
sim_score_grp	0	0	0
tail-methods	0.01	0.00	0.02
tarReduce	0	0	0
targetList	0	0	0
tsea_dup_hyperG	0.00	0.02	0.01
tsea_mGSEA	0	0	0
tsea_mabs	0.02	0.00	0.02
vec_char_redu	0	0	0

name	user	system	elapsed
add_pcid	0.02	0.00	0.02
append2H5	0.03	0.03	0.06
build_custom_db	0.26	0.03	0.30
cellNtestPlot	0.24	0.00	0.24
cell_info	0.09	0.00	0.09
chembl_moa_list	0.00	0.02	0.01
clue_moa_list	0	0	0
comp_fea_res	0.16	0.03	0.19
create_empty_h5	0.03	0.00	0.03
dim-methods	0.01	0.00	0.01
drug_cell_ranks	0.02	0.00	0.02
drugs-methods	0.02	0.00	0.02
drugs10	0	0	0
dsea_GSEA	0.01	0.00	0.01
dsea_hyperG	0.00	0.02	0.02
dtnetplot	5.78	1.00	7.15
enrichGO2	0	0	0
enrichKEGG2	0	0	0
enrichMOA	0.05	0.00	0.05
enrichReactome	0	0	0
feaResult	0	0	0
gctx2h5	0.48	0.14	0.64
gessResult	0	0	0
gess_cmap	0	0	0
gess_cor	0.00	0.02	0.02
gess_fisher	0	0	0
gess_gcmap	0	0	0
gess_lincs	0	0	0
gess_res_vis	0.30	0.01	0.31
getSig	0.47	0.03	0.50
get_targets	3.33	0.14	3.66
get_treat_info	0.03	0.00	0.03
gmt2h5	0.15	0.04	0.40
gseGO2	0	0	0
gseKEGG2	0.02	0.00	0.02
gseReactome	0	0	0
head-methods	0.01	0.00	0.02
lincs_expr_inst_info	0.06	0.00	0.06
lincs_pert_info	0.11	0.00	0.11
lincs_sig_info	0.07	0.01	0.08
list2df	0	0	0
mabsGO	0.00	0.02	0.02
mabsKEGG	0.01	0.00	0.01
mabsReactome	0.02	0.00	0.02
matrix2h5	0.09	0.00	0.17
moa_conn	0.05	0.00	0.05
parse_gctx	0.09	0.00	0.09
qSig	0.39	0.02	0.41
rand_query_ES	3.92	0.22	4.14
read_gmt	0	0	0
result-methods	0.04	0.00	0.03
runWF	32.06	1.40	39.21
set_readable	19.94	0.75	21.03
show-methods	0.03	0.00	0.03
sim_score_grp	0.02	0.00	0.02
tail-methods	0	0	0
tarReduce	0	0	0
targetList	0.00	0.02	0.02
tsea_dup_hyperG	0	0	0
tsea_mGSEA	0.00	0.01	0.01
tsea_mabs	0	0	0
vec_char_redu	0	0	0

CHECK results for signatureSearch on tokay2

Summary

Command output

Installation output

Tests output

Example timings