BioC 3.6: CHECK report for matter on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings matter_1.3.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/matter.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.3.3’
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* 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: OK

* installing *source* package ‘matter’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c matter.cpp -o matter.o
In file included from matter.cpp:4:0:
matter.h: In member function ‘index_t Atoms::write_indices(RType*, Rindex_t*, long int, size_t) [with RType = unsigned char; index_t = long int; Rindex_t = double; size_t = long unsigned int]’:
matter.h:742:20: warning: ‘numWrote’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             return numWrote;
                    ^
matter.h: In member function ‘index_t Atoms::write_indices(RType*, Rindex_t*, long int, size_t) [with RType = int; index_t = long int; Rindex_t = double; size_t = long unsigned int]’:
matter.h:742:20: warning: ‘numWrote’ may be used uninitialized in this function [-Wmaybe-uninitialized]
matter.h: In member function ‘index_t Atoms::write_indices(RType*, Rindex_t*, long int, size_t) [with RType = double; index_t = long int; Rindex_t = double; size_t = long unsigned int]’:
matter.h:742:20: warning: ‘numWrote’ 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 = 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 function ‘double var(MatterIterator<T>&, bool) [with T = int]’:
matter.cpp:3502:17: warning: ‘s_new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 s_new = s_old + (*x - m_old) * (*x - m_new);
                 ^
matter.cpp:3501:17: warning: ‘m_new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 m_new = m_old + (*x - m_old) / n;
                 ^
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 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 = long unsigned int]’:
matter.cpp:2903:25: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from matter.cpp:4:0:
matter.h: In member function ‘index_t Atoms::read_indices(RType*, Rindex_t*, long int, size_t) [with RType = double; index_t = long int; Rindex_t = double; size_t = long unsigned int]’:
matter.h:719:20: warning: ‘numRead’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             return numRead;
                    ^
matter.cpp: In function ‘double var(MatterIterator<T>&, bool) [with T = double]’:
matter.cpp:3502:17: warning: ‘s_new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 s_new = s_old + (*x - m_old) * (*x - m_new);
                 ^
matter.cpp:3501:17: warning: ‘m_new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 m_new = m_old + (*x - m_old) / n;
                 ^
In file included from matter.cpp:4:0:
matter.h: In member function ‘index_t Atoms::read_indices(RType*, Rindex_t*, long int, size_t) [with RType = unsigned char; index_t = long int; Rindex_t = double; size_t = long unsigned int]’:
matter.h:719:20: warning: ‘numRead’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             return numRead;
                    ^
matter.h: In member function ‘index_t Atoms::read_indices(RType*, Rindex_t*, long int, size_t) [with RType = int; index_t = long int; Rindex_t = double; size_t = long unsigned int]’:
matter.h:719:20: warning: ‘numRead’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o matter.so init.o matter.o utils.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/matter.Rcheck/matter/libs
** 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
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (matter)

name	user	system	elapsed
apply	0.068	0.000	0.069
bigglm	0.260	0.000	0.263
delayed-ops	0.196	0.000	0.198
drle-class	0.000	0.000	0.001
matter-class	0.024	0.000	0.027
matter_arr-class	0.004	0.000	0.006
matter_df	0.036	0.000	0.036
matter_list-class	0.012	0.000	0.012
matter_mat-class	0.004	0.000	0.006
matter_str	0.020	0.000	0.018
matter_vec-class	0.004	0.000	0.002
prcomp	0.024	0.008	0.034
profmem	0.328	0.000	0.325
scale	0.024	0.000	0.024
summary-stats	0.008	0.000	0.010

BioC 3.6: CHECK report for matter on malbec1

Summary

Command output