Multiple platform build/check report for BioC 3.12 - CHECK report for matter on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:matter.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings matter_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/matter.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.16.0’
* 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-3.12-bioc/meat/matter.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL matter
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘matter’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-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-3.12-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-3.12-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-3.12-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-3.12-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-3.12-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-3.12-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-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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)

Tests output


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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: Matrix
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")
[ FAIL 0 | WARN 486 | SKIP 0 | PASS 343 ]
> 
> proc.time()
   user  system elapsed 
 15.184   0.424  15.663

Example timings

name	user	system	elapsed
apply	0.724	0.132	0.868
biglm	0.048	0.004	0.055
binvec	0.004	0.000	0.002
bsearch	0.000	0.000	0.001
checksum	0.016	0.000	0.017
chunk_apply	0.284	0.008	0.293
colStats	0.016	0.008	0.026
combine-method	0.000	0.000	0.001
combiner-method	0.012	0.000	0.013
delayed-ops	0.008	0.000	0.009
drle-class	0	0	0
keys-method	0.012	0.000	0.008
lapply	0.036	0.000	0.036
locmax	0.000	0.000	0.001
matter-class	0.024	0.000	0.024
matter_arr-class	0.020	0.000	0.018
matter_df-class	0.096	0.000	0.098
matter_fc-class	0.032	0.000	0.032
matter_list-class	0.020	0.000	0.019
matter_mat-class	0.012	0.000	0.013
matter_str-class	0.012	0.000	0.016
matter_vec-class	0.004	0.000	0.006
prcomp	0.028	0.004	0.032
profmem	0.432	0.004	0.436
rep_vt	0.004	0.000	0.003
scale	0.016	0.000	0.018
sparse_mat-class	0.008	0.000	0.011
stream-stats	0.012	0.000	0.011
struct	0.016	0.000	0.015
summary-stats	0.020	0.000	0.019
tolerance-method	0.012	0.000	0.011
uuid	0.004	0.000	0.002
virtual_mat-class	0.012	0.000	0.012

CHECK report for matter on malbec1

Summary

Command output

Installation output

Tests output

Example timings