Package: matter

Version: 1.12.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:matter.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings matter_1.12.0.tar.gz

StartedAt: 2020-04-15 04:16:04 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:17:36 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 92.8 seconds

RetCode: 0

Status:  OK

CheckDir: matter.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:matter.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings matter_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/matter.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘matter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘matter’ version ‘1.12.0’
* 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 ‘matter’ 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/matter.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL matter
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘matter’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c altrep.cpp -o altrep.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c bsearch.cpp -o bsearch.o
bsearch.cpp: In function ‘size_t binary_search(T, SEXP, size_t, size_t, double, int, int, bool) [with T = const char*]’:
bsearch.cpp:51:36: warning: ‘result’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   else if ( mid == right && result > 0 )
                             ~~~~~~~^~~
bsearch.cpp: In function ‘size_t binary_search(T, SEXP, size_t, size_t, double, int, int, bool) [with T = double]’:
bsearch.cpp:136:27: warning: ‘diff’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   else if ( (mid == right && diff > 0) && (nearest || dright < tol) )
             ~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c init.cpp -o init.o
In file included from init.cpp:5:0:
altrep.h:20:25: warning: ‘MatterAlt_string’ defined but not used [-Wunused-variable]
 static R_altrep_class_t MatterAlt_string;
                         ^~~~~~~~~~~~~~~~
altrep.h:19:25: warning: ‘MatterAlt_real’ defined but not used [-Wunused-variable]
 static R_altrep_class_t MatterAlt_real;
                         ^~~~~~~~~~~~~~
altrep.h:18:25: warning: ‘MatterAlt_integer’ defined but not used [-Wunused-variable]
 static R_altrep_class_t MatterAlt_integer;
                         ^~~~~~~~~~~~~~~~~
altrep.h:17:25: warning: ‘MatterAlt_logical’ defined but not used [-Wunused-variable]
 static R_altrep_class_t MatterAlt_logical;
                         ^~~~~~~~~~~~~~~~~
altrep.h:16:25: warning: ‘MatterAlt_raw’ defined but not used [-Wunused-variable]
 static R_altrep_class_t MatterAlt_raw;
                         ^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -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]’:
matter.cpp:3409:33: 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]’:
matter.cpp:3409:33: 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]’:
matter.cpp:3409:33: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                         add<T,T>(x, y, i, atm, 0, count, skip);
                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
matter.cpp: In function ‘double var(MatterIterator<T>&, bool) [with T = double]’:
matter.cpp:4144:17: warning: ‘s_new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 s_new = s_old + (*x - m_old) * (*x - m_new);
                 ^~~~~
matter.cpp:4143:37: warning: ‘m_new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 m_new = m_old + (*x - m_old) / n;
                                 ~~~~^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c vectools.cpp -o vectools.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o matter.so altrep.o bsearch.o init.o matter.o utils.o vectools.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-matter/00new/matter/libs
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘apply’ in package ‘matter’
Creating a new generic function for ‘scale’ in package ‘matter’
Creating a new generic function for ‘biglm’ in package ‘matter’
** 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 (matter)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: BiocParallel
Loading required package: biglm
Loading required package: DBI

Attaching package: 'matter'

The following object is masked from 'package:biglm':

    biglm

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

    apply, scale

> 
> test_check("matter")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 330 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  7.408   0.336   7.800 

name	user	system	elapsed
apply	0.648	0.148	0.821
biglm	0.052	0.004	0.055
binvec	0.004	0.000	0.002
bsearch	0	0	0
checksum	0.016	0.000	0.016
chunk_apply	0.188	0.008	0.199
colStats	0.024	0.004	0.024
combine-method	0.000	0.000	0.001
combiner-method	0.020	0.000	0.017
delayed-ops	0.008	0.000	0.011
drle-class	0.000	0.000	0.001
keys-method	0.012	0.000	0.012
lapply	0.048	0.000	0.046
locmax	0	0	0
matter-class	0.040	0.004	0.042
matter_arr-class	0.032	0.000	0.030
matter_df-class	0.104	0.000	0.104
matter_fc-class	0.032	0.000	0.032
matter_list-class	0.02	0.00	0.02
matter_mat-class	0.012	0.000	0.012
matter_str-class	0.012	0.000	0.013
matter_vec-class	0.004	0.000	0.004
prcomp	0.032	0.000	0.030
profmem	0.468	0.000	0.471
rep_vt	0.004	0.000	0.003
scale	0.016	0.000	0.016
sparse_mat-class	0.008	0.004	0.011
stream-stats	0.012	0.000	0.013
struct	0.012	0.000	0.013
summary-stats	0.016	0.004	0.018
tolerance-method	0.012	0.000	0.010
uuid	0.000	0.000	0.001
virtual_mat-class	0.012	0.000	0.008