Multiple platform build/check report for BioC 3.7 - CHECK report for TFBSTools on tokay2

Package: TFBSTools

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFBSTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings TFBSTools_1.18.0.tar.gz

StartedAt: 2018-10-17 05:10:32 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 05:19:25 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 532.6 seconds

RetCode: 0

Status: OK

CheckDir: TFBSTools.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFBSTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings TFBSTools_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/TFBSTools.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TFBSTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TFBSTools' version '1.18.0'
* 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 'TFBSTools' 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 ... NOTE
Unexported objects imported by ':::' calls:
  'S4Vectors:::new_SimpleList_from_list' 'seqLogo:::pwm2ic'
  See the note in ?`:::` about the use of this operator.
* 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 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-3.7-bioc/R/library/TFBSTools/libs/i386/TFBSTools.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 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 or elapsed time > 5s
                       user system elapsed
SiteSetList-class     50.73   1.61   52.34
searchAln-methods      9.03   0.07    9.16
toGRangesList-methods  6.61   0.00    6.61
SiteSet-class          5.60   0.14    5.74
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
SiteSetList-class     63.17   3.03   67.64
searchAln-methods     10.23   0.02   10.25
toGRangesList-methods  9.53   0.01   10.50
SiteSet-class          8.03   0.26    8.29
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/TFBSTools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/TFBSTools_1.18.0.tar.gz && rm -rf TFBSTools.buildbin-libdir && mkdir TFBSTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TFBSTools.buildbin-libdir TFBSTools_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL TFBSTools_1.18.0.zip && rm TFBSTools_1.18.0.tar.gz TFBSTools_1.18.0.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  151k  100  151k    0     0  2473k      0 --:--:-- --:--:-- --:--:-- 2751k

install for i386

* installing *source* package 'TFBSTools' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o
matrixAlignerDynamic.c: In function 'score':
matrixAlignerDynamic.c:235:22: warning: 'best_pntr' may be used uninitialized in this function [-Wmaybe-uninitialized]
   while (current_pntr->father != NULL){ // while the father of the current pointer exists, walk through the best posible alignment
                      ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_TFBSTools.c -o R_init_TFBSTools.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o TFBSTools.dll tmp.def matrixAlignerDynamic.o R_init_TFBSTools.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/TFBSTools.buildbin-libdir/TFBSTools/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'seqLogo' in package 'TFBSTools'
** help
*** installing help indices
  converting help for package 'TFBSTools'
    finding HTML links ... done
    IUPAC2Matrix                            html  
    MA0004.1                                html  
    MotifSet-class                          html  
    PFMSimilarity-methods                   html  
    PWMSimilarity-methods                   html  
    SitePairSet-class                       html  
    SitePairSetList-class                   html  
    SiteSet-class                           html  
    SiteSetList-class                       html  
    TFBSTools-package                       html  
    TFFM-class                              html  
    XMatrix-class                           html  
    XMatrixList-class                       html  
    calConservation-methods                 html  
    deleteMatrixHavingID-methods            html  
    dmmEM-methods                           html  
    getEmissionProb                         html  
    getMatrixByID-methods                   html  
    getMatrixSet-methods                    html  
    getPosProb                              html  
    makeFlatFileDir                         html  
    parseMEMEOutput                         html  
    permuteMatrix-methods                   html  
    rPWMDmm-methods                         html  
    readJASPARMatrix                        html  
    readXMLTFFM                             html  
    runMEME-methods                         html  
    sampleRanges                            html  
    searchAln-methods                       html  
    searchPairBSgenome-methods              html  
    searchSeq-methods                       html  
    seqLogo                                 html  
    shannon.entropy                         html  
    toGRangesList-methods                   html  
    toICM-methods                           html  
    finding level-2 HTML links ... done

    toPWM-methods                           html  
    writeGFF3-methods                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'TFBSTools' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o
matrixAlignerDynamic.c: In function 'score':
matrixAlignerDynamic.c:235:22: warning: 'best_pntr' may be used uninitialized in this function [-Wmaybe-uninitialized]
   while (current_pntr->father != NULL){ // while the father of the current pointer exists, walk through the best posible alignment
                      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_TFBSTools.c -o R_init_TFBSTools.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o TFBSTools.dll tmp.def matrixAlignerDynamic.o R_init_TFBSTools.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/TFBSTools.buildbin-libdir/TFBSTools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TFBSTools' as TFBSTools_1.18.0.zip
* DONE (TFBSTools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'TFBSTools' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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(TFBSTools)

> 
> test_check("TFBSTools")
== testthat results  ===========================================================
OK: 34 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  13.89    1.09   14.96


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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(TFBSTools)

> 
> test_check("TFBSTools")
== testthat results  ===========================================================
OK: 34 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  16.15    0.65   16.93

name	user	system	elapsed
IUPAC2Matrix	0	0	0
MA0004.1	0.02	0.00	0.01
MotifSet-class	0	0	0
PFMSimilarity-methods	0.32	0.06	0.39
PWMSimilarity-methods	0.00	0.01	0.01
SiteSet-class	5.60	0.14	5.74
SiteSetList-class	50.73	1.61	52.34
TFFM-class	0.05	0.00	0.08
XMatrix-class	0.01	0.00	0.02
XMatrixList-class	0	0	0
deleteMatrixHavingID-methods	0.14	0.03	0.17
dmmEM-methods	0	0	0
getEmissionProb	0.33	0.00	0.35
getMatrixByID-methods	0.28	0.03	0.31
getMatrixSet-methods	0	0	0
getPosProb	0.27	0.03	0.30
makeFlatFileDir	0	0	0
parseMEMEOutput	0.12	0.10	0.25
permuteMatrix-methods	0.08	0.03	0.11
rPWMDmm-methods	0	0	0
readJASPARMatrix	0.00	0.03	0.03
readXMLTFFM	0.05	0.02	0.06
runMEME-methods	0	0	0
sampleRanges	0.37	0.15	0.53
searchAln-methods	9.03	0.07	9.16
searchPairBSgenome-methods	0	0	0
searchSeq-methods	1.00	0.03	1.03
seqLogo	1.74	0.15	1.89
shannon.entropy	0	0	0
toGRangesList-methods	6.61	0.00	6.61
toICM-methods	0.03	0.00	0.03
toPWM-methods	0.00	0.02	0.02

name	user	system	elapsed
IUPAC2Matrix	0	0	0
MA0004.1	0.01	0.00	0.01
MotifSet-class	0	0	0
PFMSimilarity-methods	0.33	0.05	0.37
PWMSimilarity-methods	0.02	0.00	0.02
SiteSet-class	8.03	0.26	8.29
SiteSetList-class	63.17	3.03	67.64
TFFM-class	0.05	0.00	0.05
XMatrix-class	0.02	0.00	0.01
XMatrixList-class	0.02	0.00	0.02
deleteMatrixHavingID-methods	0.12	0.05	0.17
dmmEM-methods	0	0	0
getEmissionProb	0.29	0.00	0.30
getMatrixByID-methods	0.22	0.06	0.28
getMatrixSet-methods	0	0	0
getPosProb	0.27	0.00	0.27
makeFlatFileDir	0	0	0
parseMEMEOutput	0.11	0.00	0.11
permuteMatrix-methods	0.04	0.02	0.06
rPWMDmm-methods	0	0	0
readJASPARMatrix	0.04	0.00	0.03
readXMLTFFM	0.03	0.00	0.03
runMEME-methods	0	0	0
sampleRanges	0.25	0.00	0.25
searchAln-methods	10.23	0.02	10.25
searchPairBSgenome-methods	0	0	0
searchSeq-methods	1.09	0.04	1.14
seqLogo	2.94	0.16	3.46
shannon.entropy	0	0	0
toGRangesList-methods	9.53	0.01	10.50
toICM-methods	0.00	0.02	0.01
toPWM-methods	0.02	0.00	0.02

CHECK report for TFBSTools on tokay2

Summary

Command output

Installation output

Tests output

Example timings