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CHECK report for BUSpaRse on tokay1

This page was generated on 2020-08-05 11:39:30 -0400 (Wed, 05 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BUSpaRse PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 211/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUSpaRse 1.3.1
Lambda Moses
Snapshot Date: 2020-08-04 14:50:10 -0400 (Tue, 04 Aug 2020)
URL: https://git.bioconductor.org/packages/BUSpaRse
Branch: master
Last Commit: 3c9922c
Last Changed Date: 2020-06-02 19:36:58 -0400 (Tue, 02 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BUSpaRse
Version: 1.3.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BUSpaRse.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BUSpaRse_1.3.1.tar.gz
StartedAt: 2020-08-05 05:47:27 -0400 (Wed, 05 Aug 2020)
EndedAt: 2020-08-05 06:04:26 -0400 (Wed, 05 Aug 2020)
EllapsedTime: 1018.7 seconds
RetCode: 0
Status:  OK  
CheckDir: BUSpaRse.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BUSpaRse.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BUSpaRse_1.3.1.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BUSpaRse.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BUSpaRse/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BUSpaRse' version '1.3.1'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'BUSpaRse' 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
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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-3.12-bioc/R/library/BUSpaRse/libs/i386/BUSpaRse.dll':
  Found '_exit', possibly from '_exit' (C)
  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-3.12-bioc/R/library/BUSpaRse/libs/x64/BUSpaRse.dll':
  Found '_exit', possibly from '_exit' (C)
  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
knee_plot        49.30   2.64   86.39
tr2g_TxDb        39.89   3.34   43.28
transcript2gene  22.52   0.14   30.50
dl_transcriptome 20.39   0.70   30.80
tr2g_EnsDb        5.44   2.50    7.94
tr2g_ensembl      7.41   0.05   33.19
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
knee_plot        44.66   2.67   65.68
tr2g_TxDb        43.69   3.39   47.16
dl_transcriptome 19.19   0.70   26.27
transcript2gene  19.50   0.17   27.34
tr2g_ensembl      6.83   0.02   13.11
tr2g_EnsDb        4.99   1.80    6.78
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BUSpaRse.Rcheck/00check.log'
for details.



Installation output

BUSpaRse.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BUSpaRse_1.3.1.tar.gz && rm -rf BUSpaRse.buildbin-libdir && mkdir BUSpaRse.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BUSpaRse.buildbin-libdir BUSpaRse_1.3.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BUSpaRse_1.3.1.zip && rm BUSpaRse_1.3.1.tar.gz BUSpaRse_1.3.1.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
100 88658  100 88658    0     0  2566k      0 --:--:-- --:--:-- --:--:-- 2886k

install for i386

* installing *source* package 'BUSpaRse' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppProgress/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp    -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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppProgress/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fill_cell_gene.cpp -o fill_cell_gene.o
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/iterator/iterator_adaptor.hpp:14,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/token_iterator.hpp:22,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/tokenizer.hpp:20,
                 from fill_cell_gene.cpp:16:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o BUSpaRse.dll tmp.def RcppExports.o fill_cell_gene.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BUSpaRse.buildbin-libdir/00LOCK-BUSpaRse/00new/BUSpaRse/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BUSpaRse'
    finding HTML links ... done
    EC2gene                                 html  
    annot_circular                          html  
    finding level-2 HTML links ... done

    annots_from_fa_df                       html  
    cellranger_biotypes                     html  
    check_char1                             html  
    check_genome                            html  
    check_gff                               html  
    check_tag_present                       html  
    check_tx                                html  
    dl_transcriptome                        html  
    dot-get_velocity_files                  html  
    ensembl_gene_biotypes                   html  
    ensembl_gff_mcols                       html  
    ensembl_gtf_mcols                       html  
    ensembl_tx_biotypes                     html  
    get_intron_flanks                       html  
    get_velocity_files                      html  
    knee_plot                               html  
    make_sparse_matrix                      html  
    match_style                             html  
    read_count_output                       html  
    read_velocity_output                    html  
    refseq_gff_mcols                        html  
    save_tr2g_bustools                      html  
    sort_tr2g                               html  
    species2dataset                         html  
    standardize_tags                        html  
    sub_annot                               html  
    subset_annot                            html  
    tr2g_EnsDb                              html  
    tr2g_GRanges                            html  
    tr2g_TxDb                               html  
    tr2g_ensembl                            html  
    tr2g_fasta                              html  
    tr2g_gff3                               html  
    tr2g_gtf                                html  
    tr2g_junction                           html  
    transcript2gene                         html  
    validate_velocity_input                 html  
    write_velocity_output                   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 'BUSpaRse' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppProgress/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp    -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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppProgress/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fill_cell_gene.cpp -o fill_cell_gene.o
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/iterator/iterator_adaptor.hpp:14,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/token_iterator.hpp:22,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/tokenizer.hpp:20,
                 from fill_cell_gene.cpp:16:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BUSpaRse.dll tmp.def RcppExports.o fill_cell_gene.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BUSpaRse.buildbin-libdir/BUSpaRse/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BUSpaRse' as BUSpaRse_1.3.1.zip
* DONE (BUSpaRse)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BUSpaRse' successfully unpacked and MD5 sums checked

Tests output

BUSpaRse.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(BUSpaRse)
> 
> test_check("BUSpaRse")
== testthat results  ===========================================================
[ OK: 104 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  71.68    3.89   93.90 

BUSpaRse.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(BUSpaRse)
> 
> test_check("BUSpaRse")
== testthat results  ===========================================================
[ OK: 104 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  58.20    1.32   75.78 

Example timings

BUSpaRse.Rcheck/examples_i386/BUSpaRse-Ex.timings

nameusersystemelapsed
EC2gene0.120.000.22
annots_from_fa_df0.240.000.24
dl_transcriptome20.39 0.7030.80
get_velocity_files1.610.351.95
knee_plot49.30 2.6486.39
make_sparse_matrix000
read_count_output0.010.000.02
read_velocity_output000
save_tr2g_bustools0.600.000.59
sort_tr2g0.450.040.50
species2dataset000
subset_annot1.780.252.03
tr2g_EnsDb5.442.507.94
tr2g_TxDb39.89 3.3443.28
tr2g_ensembl 7.41 0.0533.19
tr2g_fasta0.000.020.02
tr2g_gff31.800.232.03
tr2g_gtf0.590.020.61
transcript2gene22.52 0.1430.50

BUSpaRse.Rcheck/examples_x64/BUSpaRse-Ex.timings

nameusersystemelapsed
EC2gene0.170.003.45
annots_from_fa_df0.370.000.38
dl_transcriptome19.19 0.7026.27
get_velocity_files3.650.033.69
knee_plot44.66 2.6765.68
make_sparse_matrix000
read_count_output0.010.000.02
read_velocity_output000
save_tr2g_bustools0.470.070.53
sort_tr2g0.600.010.61
species2dataset000
subset_annot1.860.282.14
tr2g_EnsDb4.991.806.78
tr2g_TxDb43.69 3.3947.16
tr2g_ensembl 6.83 0.0213.11
tr2g_fasta0.040.000.04
tr2g_gff31.460.121.58
tr2g_gtf1.000.051.05
transcript2gene19.50 0.1727.34