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CHECK report for matter on tokay1

This page was generated on 2018-04-12 13:28:53 -0400 (Thu, 12 Apr 2018).

Package 793/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
matter 1.4.1
Kylie A. Bemis
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/matter
Branch: RELEASE_3_6
Last Commit: ec72f93
Last Changed Date: 2017-11-02 17:56:24 -0400 (Thu, 02 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: matter
Version: 1.4.1
Command: rm -rf matter.buildbin-libdir matter.Rcheck && mkdir matter.buildbin-libdir matter.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=matter.buildbin-libdir matter_1.4.1.tar.gz >matter.Rcheck\00install.out 2>&1 && cp matter.Rcheck\00install.out matter-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=matter.buildbin-libdir --install="check:matter-install.out" --force-multiarch --no-vignettes --timings matter_1.4.1.tar.gz
StartedAt: 2018-04-12 01:09:34 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:11:41 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 127.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: matter.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf matter.buildbin-libdir matter.Rcheck && mkdir matter.buildbin-libdir matter.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=matter.buildbin-libdir matter_1.4.1.tar.gz >matter.Rcheck\00install.out 2>&1 && cp matter.Rcheck\00install.out matter-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=matter.buildbin-libdir --install="check:matter-install.out" --force-multiarch --no-vignettes --timings matter_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/matter.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'matter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'matter' version '1.4.1'
* 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 'matter' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/apply.Rd:28: missing file link 'colMeans,matter_mat-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/apply.Rd:28: missing file link 'rowMeans,matter_mat-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/delayed-ops.rd:108: missing file link 'Arith'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/delayed-ops.rd:109: missing file link 'Compare'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/delayed-ops.rd:110: missing file link 'Math'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/summary-stats.Rd:79: missing file link 'colMeans'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/summary-stats.Rd:80: missing file link 'rowSums'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/summary-stats.Rd:81: missing file link 'rowMeans'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/matter.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
* 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 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-3.6-bioc/meat/matter.buildbin-libdir/matter/libs/i386/matter.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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/matter.Rcheck/00check.log'
for details.

Installation output

matter.Rcheck/00install.out


install for i386

* installing *source* package 'matter' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c matter.cpp -o matter.o
matter.cpp: In member function 'void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = int; index_t = long int; size_t = unsigned int]':
matter.cpp:2903:25: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized]
                         add<T,T>(x, y, i, atm, 0, count, skip);
                         ^
matter.cpp: In member function 'void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = unsigned char; index_t = long int; size_t = unsigned int]':
matter.cpp:2903:25: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized]
matter.cpp: In member function 'void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = double; index_t = long int; size_t = unsigned int]':
matter.cpp:2903:25: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized]
matter.cpp: In function 'double var(MatterIterator<T>&, bool) [with T = double]':
matter.cpp:3538:17: warning: 's_new' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 s_new = s_old + (*x - m_old) * (*x - m_new);
                 ^
matter.cpp:3537:17: warning: 'm_new' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 m_new = m_old + (*x - m_old) / n;
                 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o matter.dll tmp.def init.o matter.o utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/matter.buildbin-libdir/matter/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'apply' in package 'matter'
Creating a new generic function for 'scale' in package 'matter'
** help
*** installing help indices
  converting help for package 'matter'
    finding HTML links ... done
    apply                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/apply.Rd:28: missing file link 'colMeans,matter_mat-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/apply.Rd:28: missing file link 'rowMeans,matter_mat-method'
    bigglm                                  html  
    delayed-ops                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/delayed-ops.rd:108: missing file link 'Arith'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/delayed-ops.rd:109: missing file link 'Compare'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/delayed-ops.rd:110: missing file link 'Math'
    drle-class                              html  
    matter-class                            html  
    matter_arr-class                        html  
    matter_df-class                         html  
    matter_ex                               html  
    matter_fc-class                         html  
    matter_list-class                       html  
    matter_mat-class                        html  
    matter_str-class                        html  
    matter_vec-class                        html  
    prcomp                                  html  
    profmem                                 html  
    scale                                   html  
    summary-stats                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/summary-stats.Rd:79: missing file link 'colMeans'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/summary-stats.Rd:80: missing file link 'rowSums'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWjdr5/R.INSTALL1b78e5b2e36/matter/man/summary-stats.Rd:81: missing file link 'rowMeans'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'matter' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c matter.cpp -o matter.o
matter.cpp: In member function 'void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = double; index_t = long int; size_t = long long unsigned int]':
matter.cpp:2903:25: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized]
                         add<T,T>(x, y, i, atm, 0, count, skip);
                         ^
matter.cpp: In member function 'void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = int; index_t = long int; size_t = long long unsigned int]':
matter.cpp:2903:25: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized]
matter.cpp: In member function 'void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = unsigned char; index_t = long int; size_t = long long unsigned int]':
matter.cpp:2903:25: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized]
matter.cpp: In function 'double var(MatterIterator<T>&, bool) [with T = double]':
matter.cpp:3538:17: warning: 's_new' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 s_new = s_old + (*x - m_old) * (*x - m_new);
                 ^
matter.cpp:3537:17: warning: 'm_new' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 m_new = m_old + (*x - m_old) / n;
                 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o matter.dll tmp.def init.o matter.o utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/matter.buildbin-libdir/matter/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'matter' as matter_1.4.1.zip
* DONE (matter)
In R CMD INSTALL
In R CMD INSTALL

Tests output

matter.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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(matter)
Loading required package: biglm
Loading required package: DBI

Attaching package: 'matter'

The following objects are masked from 'package:base':

    apply, scale

> 
> test_check("matter")
== testthat results  ===========================================================
OK: 114 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   2.62    0.14    3.67

matter.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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(matter)
Loading required package: biglm
Loading required package: DBI

Attaching package: 'matter'

The following objects are masked from 'package:base':

    apply, scale

> 
> test_check("matter")
== testthat results  ===========================================================
OK: 114 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.32    0.14    3.87

Example timings

matter.Rcheck/examples_i386/matter-Ex.timings

nameusersystemelapsed
apply0.080.000.08
bigglm0.250.000.25
delayed-ops0.040.020.25
drle-class000
matter-class0.070.000.06
matter_arr-class0.010.000.02
matter_df-class0.050.000.04
matter_fc-class0.020.000.01
matter_list-class0.030.000.04
matter_mat-class0.000.010.01
matter_str-class0.030.000.03
matter_vec-class000
prcomp0.060.000.07
profmem0.300.000.29
scale0.030.000.03
summary-stats0.000.020.02

matter.Rcheck/examples_x64/matter-Ex.timings

nameusersystemelapsed
apply0.060.020.07
bigglm0.250.000.25
delayed-ops0.030.000.62
drle-class000
matter-class0.050.000.05
matter_arr-class0.010.000.02
matter_df-class0.030.000.03
matter_fc-class0.020.000.01
matter_list-class0.010.000.02
matter_mat-class0.020.000.01
matter_str-class0.020.000.02
matter_vec-class000
prcomp0.030.000.03
profmem0.250.000.25
scale0.030.000.03
summary-stats0.010.000.02