Package: rMAT

Version: 3.33.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rMAT.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rMAT_3.33.0.tar.gz

StartedAt: 2018-11-07 07:19:36 -0500 (Wed, 07 Nov 2018)

EndedAt: 2018-11-07 07:20:30 -0500 (Wed, 07 Nov 2018)

EllapsedTime: 53.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: rMAT.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rMAT.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rMAT_3.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rMAT.Rcheck’
* using R Under development (unstable) (2018-10-16 r75448)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rMAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rMAT’ version ‘3.33.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rMAT’ can be installed ... WARNING
Found the following significant warnings:
  BARReader.cpp:46:8: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 4 [-Wformat-truncation=]
  /usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: warning: ‘int __builtin___snprintf_chk(char*, long unsigned int, int, long unsigned int, const char*, ...)’: specified bound 255 exceeds the size 10 of the destination [-Wstringop-overflow=]
  NormalizeProbes.c:1030:18: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/rMAT.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘IRanges’ ‘Biobase’ ‘affxparser’
A package should be listed in only one of these fields.
* 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 ... NOTE
callEnrichedRegions: no visible global function definition for ‘is’
callEnrichedRegions: no visible global function definition for ‘space’
callEnrichedRegions: no visible global function definition for
  ‘IRanges’
callEnrichedRegions: no visible global function definition for
  ‘RangedData’
computeMATScore: no visible global function definition for ‘IRanges’
computeMATScore: no visible global function definition for ‘RangedData’
Undefined global functions or variables:
  IRanges RangedData is space
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in shell scripts ... 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 is not available
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/rMAT/libs/rMAT.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (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 files in ‘vignettes’ ... OK
* checking examples ... 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, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/rMAT.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL rMAT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘rMAT’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dispatch/dispatch.h usability... no
checking dispatch/dispatch.h presence... no
checking for dispatch/dispatch.h... no
checking omp.h usability... yes
checking omp.h presence... yes
checking for omp.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c BARFileData.cpp -o BARFileData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c BARFileWriter.cpp -o BARFileWriter.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c BARReader.cpp -o BARReader.o
BARReader.cpp: In function ‘SEXPREC* Parser(SEXP)’:
BARReader.cpp:259:6: warning: unused variable ‘buf’ [-Wunused-variable]
 char buf[MAX_SIZE];
      ^˜˜
BARReader.cpp: In function ‘SEXPREC* ParseMATBar(SEXP)’:
BARReader.cpp:473:42: warning: unused variable ‘regionR’ [-Wunused-variable]
  SEXP chromosomeR, positionR, matScoreR, regionR, pValueR;
                                          ^˜˜˜˜˜˜
BARReader.cpp:474:49: warning: unused variable ‘p_region’ [-Wunused-variable]
  int *p_chromosome = NULL, *p_position = NULL, *p_region = NULL;
                                                 ^˜˜˜˜˜˜˜
BARReader.cpp: In function ‘SEXPREC* ParseNormalizeBar(SEXP)’:
BARReader.cpp:587:10: warning: variable ‘p_signal’ set but not used [-Wunused-but-set-variable]
  double *p_signal = NULL;
          ^˜˜˜˜˜˜˜
BARReader.cpp: In function ‘SEXPREC* Parser(SEXP)’:
BARReader.cpp:46:8: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 4 [-Wformat-truncation=]
   SEXP Parser (SEXP fileName)
        ^˜˜˜˜˜
BARReader.cpp:46:8: note: directive argument in the range [1, 2147483646]
In file included from /usr/include/stdio.h:862:0,
                 from /usr/include/c++/7/cstdio:42,
                 from /usr/include/c++/7/ext/string_conversions.h:43,
                 from /usr/include/c++/7/bits/basic_string.h:6352,
                 from /usr/include/c++/7/string:52,
                 from /usr/include/c++/7/bits/locale_classes.h:40,
                 from /usr/include/c++/7/bits/ios_base.h:41,
                 from /usr/include/c++/7/ios:42,
                 from /usr/include/c++/7/ostream:38,
                 from /usr/include/c++/7/iostream:39,
                 from BARReader.cpp:26:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: ‘__builtin___snprintf_chk’ output between 8 and 17 bytes into a destination of size 10
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
In function ‘int snprintf(char*, size_t, const char*, ...)’,
    inlined from ‘SEXPREC* Parser(SEXP)’ at BARReader.cpp:260:9:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: warning: ‘int __builtin___snprintf_chk(char*, long unsigned int, int, long unsigned int, const char*, ...)’: specified bound 255 exceeds the size 10 of the destination [-Wstringop-overflow=]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c BARWriter.cpp -o BARWriter.o
BARWriter.cpp: In function ‘SEXPREC* WriteBAR(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
BARWriter.cpp:90:9: warning: unused variable ‘signal2Length’ [-Wunused-variable]
     int signal2Length = length(pValue);
         ^˜˜˜˜˜˜˜˜˜˜˜˜
BARWriter.cpp:93:10: warning: unused variable ‘lengthList’ [-Wunused-variable]
     int *lengthList = new int[NUM_SEQ];
          ^˜˜˜˜˜˜˜˜˜
BARWriter.cpp:94:9: warning: unused variable ‘curListPtr’ [-Wunused-variable]
     int curListPtr = 0, startListPtr = 0;
         ^˜˜˜˜˜˜˜˜˜
BARWriter.cpp:94:25: warning: unused variable ‘startListPtr’ [-Wunused-variable]
     int curListPtr = 0, startListPtr = 0;
                         ^˜˜˜˜˜˜˜˜˜˜˜
BARWriter.cpp:95:9: warning: unused variable ‘curChromosome’ [-Wunused-variable]
     int curChromosome = INTEGER(chNos)[0];
         ^˜˜˜˜˜˜˜˜˜˜˜˜
BARWriter.cpp:96:9: warning: unused variable ‘i’ [-Wunused-variable]
     int i;
         ^
BARWriter.cpp: In function ‘SEXPREC* WriteNormalizedBAR(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
BARWriter.cpp:274:6: warning: unused variable ‘addPos’ [-Wunused-variable]
  int addPos = 0;
      ^˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c BPMAPFileData.cpp -o BPMAPFileData.o
BPMAPFileData.cpp: In member function ‘bool affxbpmap::CBPMAPFileData::ReadDataSection()’:
BPMAPFileData.cpp:379:7: warning: unused variable ‘hitSize’ [-Wunused-variable]
   int hitSize=(m_SequenceItems[iSeq].m_ProbePairs == PM_MM ? HIT_ITEM_SIZE_WITH_PROBE_PAIRS : HIT_ITEM_SIZE_WITH_PM_ONLY);
       ^˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c BPMAPfunctions.cpp -o BPMAPfunctions.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c DeclareAll.c -o DeclareAll.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c FileIO.cpp -o FileIO.o
FileIO.cpp: In function ‘float MmGetFloat_I(float*)’:
FileIO.cpp:362:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   return *((float*)&v);
                      ^
In file included from FileIO.cpp:27:0:
FileIO.cpp: In function ‘void MmSetFloat_I(float*, float)’:
FileIO.cpp:367:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   *(uint32_t*)ptr=htoil(*(uint32_t*)&val);
                                      ^
FileIO.h:90:19: note: in definition of macro ‘htoil’
 #define htoil(x) (x)
                   ^
FileIO.cpp: In function ‘float MmGetFloat_N(float*)’:
FileIO.cpp:373:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   return *((float*)&v);
                      ^
In file included from FileIO.cpp:36:0:
FileIO.cpp: In function ‘void MmSetFloat_N(float*, float)’:
FileIO.cpp:378:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   *(uint32_t*)ptr=htonl(*(uint32_t*)&val);
                                      ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c FileWriter.cpp -o FileWriter.o
FileWriter.cpp: In function ‘void WriteFloat_I(std::ofstream&, float)’:
FileWriter.cpp:108:42: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  WriteUInt32_I(outstr,*(uint32_t *)(&fval));
                                          ^
FileWriter.cpp: In function ‘void WriteFloat_N(std::ofstream&, float)’:
FileWriter.cpp:113:42: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  WriteUInt32_N(outstr,*(uint32_t *)(&fval));
                                          ^
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c NormalizeProbes.c -o NormalizeProbes.o
NormalizeProbes.c: In function ‘NormalizeProbes’:
NormalizeProbes.c:91:13: warning: unused variable ‘j’ [-Wunused-variable]
         int j=0,nVariables;
             ^
NormalizeProbes.c: In function ‘normArray’:
NormalizeProbes.c:1030:18: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
         else if(k==iterMax & i>=(*nProbes))
                 ˜^˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o rMAT.so BARFileData.o BARFileWriter.o BARReader.o BARWriter.o BPMAPFileData.o BPMAPfunctions.o DeclareAll.o FileIO.o FileWriter.o NormalizeProbes.o -lgsl -lgslcblas -lm -lgomp -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/rMAT/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rMAT)

name	user	system	elapsed
BPMAPCelParser	0.283	0.008	0.333
MATScore	0	0	0
NormalizeProbes	0.479	0.011	0.367
ReadBPMAPAllSeqHeader	0.009	0.000	0.009
callEnrichedRegions	0.667	0.005	0.568
computeMATScore	0.518	0.016	0.444
tillingSet	0.100	0.000	0.101