BioC 3.1: CHECK report for PING on moscato2

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### Running command:
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###   rm -rf PING.buildbin-libdir PING.Rcheck && mkdir PING.buildbin-libdir PING.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PING.buildbin-libdir PING_2.12.0.tar.gz >PING.Rcheck\00install.out 2>&1 && cp PING.Rcheck\00install.out PING-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=PING.buildbin-libdir --install="check:PING-install.out" --force-multiarch --no-vignettes --timings PING_2.12.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/PING.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PING/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PING' version '2.12.0'
* 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 whether package 'PING' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
    libs      1.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'IRanges'
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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'BSgenome' 'BiocGenerics' 'fda' 'methods'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'GenomicRanges' 'chipseq'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'parallel:::detectCores' 'parallel:::makeCluster'
  'parallel:::parLapply' 'parallel:::stopCluster'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot,ping-segReads : .local: warning in symbols((map[, 1] + map[,
  2])/2, rep(0.35, nMap), rectangle = cbind(map[, 2] - map[, 1],
  rep(0.6, nMap)), inches = FALSE, bg = grey(0.6), fg = 0, add = TRUE,
  xlim = c(m, M), ylim = c(0, 1)): partial argument match of
  'rectangle' to 'rectangles'
plot,ping-segReads : .local : <anonymous>: warning in
  symbols(x@estimates$mu + shift * se(x), rep(0.5, K), rec =
  matrix(rep(c(147, 0.8), K), ncol = 2, byrow = TRUE), inches = FALSE,
  bg = 0, fg = grey(abs(shift) * se(x)/(3 * (se(x)))), add = TRUE, xlim
  = c(m, M), ylim = c(0, 1), lwd = 2): partial argument match of 'rec'
  to 'rectangles'
plot,ping-segReads : .local: warning in symbols(x@estimates$mu,
  rep(0.5, K), rec = matrix(rep(c(147, 0.8), K), ncol = 2, byrow =
  TRUE), inches = FALSE, bg = "white", fg = grey(abs(0)), add = TRUE,
  xlim = c(m, M), ylim = c(0, 1)): partial argument match of 'rec' to
  'rectangles'
CoverageTrack: no visible global function definition for 'seqnames'
RawReadsTrack: no visible global function definition for 'seqnames'
RawReadsTrack: no visible global function definition for 'strand'
segmentPING: no visible global function definition for 'seqlevels'
plot,data.frame-data.frame : .local: no visible global function
  definition for 'pingFDR2'
plot,pingList-pingList : .local: no visible global function definition
  for 'pingFDR'
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.1-bioc/meat/PING.buildbin-libdir/PING/libs/i386/PING.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-3.1-bioc/meat/PING.buildbin-libdir/PING/libs/x64/PING.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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' ... [13s] OK
** running examples for arch 'x64' ... [15s] 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: 6 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/PING.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'PING' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -IC:/GSL/i386/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -IC:/GSL/i386/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ping.c -o ping.o
ping.c: In function 'fitModelAllk':
ping.c:145:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c: In function 'iterEM':
ping.c:659:25: warning: unused variable 'mu' [-Wunused-variable]
ping.c: In function 'ECM1':
ping.c:912:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:1072:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:760:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'ECM1PE':
ping.c:1320:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:1473:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:1108:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'ECM2':
ping.c:1536:66: warning: unused variable 'ee' [-Wunused-variable]
ping.c:1536:57: warning: unused variable 'ggR' [-Wunused-variable]
ping.c:1536:52: warning: unused variable 'ggF' [-Wunused-variable]
ping.c:1536:47: warning: unused variable 'aaR' [-Wunused-variable]
ping.c:1536:42: warning: unused variable 'aaF' [-Wunused-variable]
ping.c:1536:29: warning: unused variable 'etaDiff' [-Wunused-variable]
ping.c:1536:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
ping.c:1527:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'ECM2PE':
ping.c:1743:66: warning: unused variable 'ee' [-Wunused-variable]
ping.c:1743:57: warning: unused variable 'ggR' [-Wunused-variable]
ping.c:1743:52: warning: unused variable 'ggF' [-Wunused-variable]
ping.c:1743:47: warning: unused variable 'aaR' [-Wunused-variable]
ping.c:1743:42: warning: unused variable 'aaF' [-Wunused-variable]
ping.c:1743:29: warning: unused variable 'etaDiff' [-Wunused-variable]
ping.c:1734:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'getInfMat':
ping.c:2590:80: warning: unused variable 'PhiRw' [-Wunused-variable]
ping.c:2590:73: warning: unused variable 'PhiFw' [-Wunused-variable]
ping.c: In function 'getInfMatPE':
ping.c:3040:59: warning: unused variable 'PhiFRw' [-Wunused-variable]
ping.c: In function 'mergePeak':
ping.c:3312:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable]
ping.c:3301:11: warning: unused variable 'j' [-Wunused-variable]
ping.c:3301:7: warning: unused variable 'i' [-Wunused-variable]
ping.c: In function 'BIC':
ping.c:2101:6: warning: 'penalty' may be used uninitialized in this function [-Wuninitialized]
ping.c: In function 'BICPE':
ping.c:2208:6: warning: 'penalty' may be used uninitialized in this function [-Wuninitialized]
ping.c: In function 'fitModelK':
ping.c:477:18: warning: 'firstFit' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -shared -s -static-libgcc -o PING.dll tmp.def init.o ping.o -lws2_32 -LC:/GSL/i386/lib -lgsl -lgslcblas -lm -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/PING.buildbin-libdir/PING/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'PING' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -IC:/GSL/x64/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -IC:/GSL/x64/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ping.c -o ping.o
ping.c: In function 'fitModelAllk':
ping.c:145:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c: In function 'iterEM':
ping.c:659:25: warning: unused variable 'mu' [-Wunused-variable]
ping.c: In function 'ECM1':
ping.c:912:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:1072:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:760:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'ECM1PE':
ping.c:1320:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:1473:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:1108:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'ECM2':
ping.c:1536:66: warning: unused variable 'ee' [-Wunused-variable]
ping.c:1536:57: warning: unused variable 'ggR' [-Wunused-variable]
ping.c:1536:52: warning: unused variable 'ggF' [-Wunused-variable]
ping.c:1536:47: warning: unused variable 'aaR' [-Wunused-variable]
ping.c:1536:42: warning: unused variable 'aaF' [-Wunused-variable]
ping.c:1536:29: warning: unused variable 'etaDiff' [-Wunused-variable]
ping.c:1536:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
ping.c:1527:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'ECM2PE':
ping.c:1743:66: warning: unused variable 'ee' [-Wunused-variable]
ping.c:1743:57: warning: unused variable 'ggR' [-Wunused-variable]
ping.c:1743:52: warning: unused variable 'ggF' [-Wunused-variable]
ping.c:1743:47: warning: unused variable 'aaR' [-Wunused-variable]
ping.c:1743:42: warning: unused variable 'aaF' [-Wunused-variable]
ping.c:1743:29: warning: unused variable 'etaDiff' [-Wunused-variable]
ping.c:1734:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'getInfMat':
ping.c:2590:80: warning: unused variable 'PhiRw' [-Wunused-variable]
ping.c:2590:73: warning: unused variable 'PhiFw' [-Wunused-variable]
ping.c: In function 'getInfMatPE':
ping.c:3040:59: warning: unused variable 'PhiFRw' [-Wunused-variable]
ping.c: In function 'mergePeak':
ping.c:3312:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable]
ping.c:3301:11: warning: unused variable 'j' [-Wunused-variable]
ping.c:3301:7: warning: unused variable 'i' [-Wunused-variable]
ping.c: In function 'BIC':
ping.c:2101:6: warning: 'penalty' may be used uninitialized in this function [-Wuninitialized]
ping.c: In function 'BICPE':
ping.c:2208:6: warning: 'penalty' may be used uninitialized in this function [-Wuninitialized]
ping.c: In function 'fitModelK':
ping.c:477:18: warning: 'firstFit' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -shared -s -static-libgcc -o PING.dll tmp.def init.o ping.o -lws2_32 -LC:/GSL/x64/lib -lgsl -lgslcblas -lm -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/PING.buildbin-libdir/PING/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'PING' as PING_2.12.0.zip
* DONE (PING)

name	user	system	elapsed
ping-class	0	0	0
pingError-class	0	0	0
pingList-class	0	0	0
segmentPING	0.86	0.00	0.87

name	user	system	elapsed
ping-class	0.01	0.00	0.01
pingError-class	0	0	0
pingList-class	0	0	0
segmentPING	0.95	0.01	1.32

BioC 3.1: CHECK report for PING on moscato2

Summary

Command output