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BioC 3.4: CHECK report for FunChIP on moscato1

This page was generated on 2016-09-21 03:48:31 -0700 (Wed, 21 Sep 2016).

Package 444/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FunChIP 0.99.3
Alice Parodi
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FunChIP
Last Changed Rev: 118254 / Revision: 121152
Last Changed Date: 2016-06-07 10:33:13 -0700 (Tue, 07 Jun 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: FunChIP
Version: 0.99.3
Command: rm -rf FunChIP.buildbin-libdir FunChIP.Rcheck && mkdir FunChIP.buildbin-libdir FunChIP.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FunChIP.buildbin-libdir FunChIP_0.99.3.tar.gz >FunChIP.Rcheck\00install.out 2>&1 && cp FunChIP.Rcheck\00install.out FunChIP-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=FunChIP.buildbin-libdir --install="check:FunChIP-install.out" --force-multiarch --no-vignettes --timings FunChIP_0.99.3.tar.gz
StartedAt: 2016-09-20 08:32:13 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:36:40 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 266.6 seconds
RetCode: 0
Status:  OK  
CheckDir: FunChIP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf FunChIP.buildbin-libdir FunChIP.Rcheck && mkdir FunChIP.buildbin-libdir FunChIP.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FunChIP.buildbin-libdir FunChIP_0.99.3.tar.gz >FunChIP.Rcheck\00install.out 2>&1 && cp FunChIP.Rcheck\00install.out FunChIP-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=FunChIP.buildbin-libdir --install="check:FunChIP-install.out" --force-multiarch --no-vignettes --timings FunChIP_0.99.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/FunChIP.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FunChIP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FunChIP' version '0.99.3'
* 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 whether package 'FunChIP' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 24.5Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata  21.5Mb
    libs      1.5Mb
* 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
* 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 ... 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 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/FunChIP.buildbin-libdir/FunChIP/libs/i386/FunChIP.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: 'BiocStyle'
* 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: 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/FunChIP.Rcheck/00check.log'
for details.

FunChIP.Rcheck/00install.out:


install for i386

* installing *source* package 'FunChIP' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include -I. -DNDEBUG   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c kmean_function.cpp -o kmean_function.o
kmean_function.cpp: In function 'SEXPREC* kmean_function(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
kmean_function.cpp:75:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned int i =0 ; i<num_data; i++){
                               ^
kmean_function.cpp:81:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int t =0 ; t < num_points; t++)
                                  ^
kmean_function.cpp: In function 'SEXPREC* distance_matrix(SEXP, SEXP, SEXP, SEXP, SEXP)':
kmean_function.cpp:211:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int i =0 ; i<num_data; i++){
                                   ^
kmean_function.cpp:217:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (unsigned int t =0 ; t < num_points; t++)
                                        ^
kmean_function.cpp: In function 'void kma_discrete(std::vector<peak>&, const int&, std::vector<int>&, const double&, const double&, const int&, const char&, const double&, const double&, std::vector<int>&, std::vector<double>&, std::vector<int>&, const double&, const double&, int, char, char)':
kmean_function.cpp:639:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while( iter < iter_max and number_distances_low < dati.size()  and cluster_vuoti==0){  //and number_clusters_different > 0
                                                   ^
kmean_function.cpp:678:52: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
       if ( (unsigned int)number_clusters_different == dati.size() & iter != 1)
                                                    ^
kmean_function.cpp:682:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (number_distances_low== dati.size())
                               ^
kmean_function.cpp: In function 'void normalize_data(std::vector<int>&, std::vector<int>&, const int&)':
kmean_function.cpp:760:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int i=0; i<n_clust; i++)
                           ^
In file included from kmean_function.cpp:1:0:
peak.h: In function 'void distance_L2_union(const peak&, const peak&, const double&, const double&, std::vector<double>&, int, char)':
peak.h:184:38: warning: 'D' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 area_def[0] = area[0]/D;
                                      ^
peak.h:130:17: note: 'D' was declared here
             int D;
                 ^
peak.h: In function 'void distance_L2_intersected(const peak&, const peak&, std::vector<double>&, int, char)':
peak.h:184:38: warning: 'D' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 area_def[0] = area[0]/D;
                                      ^
peak.h:130:17: note: 'D' was declared here
             int D;
                 ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o FunChIP.dll tmp.def kmean_function.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/FunChIP.buildbin-libdir/FunChIP/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'FunChIP' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include -I. -DNDEBUG   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c kmean_function.cpp -o kmean_function.o
kmean_function.cpp: In function 'SEXPREC* kmean_function(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
kmean_function.cpp:75:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned int i =0 ; i<num_data; i++){
                               ^
kmean_function.cpp:81:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int t =0 ; t < num_points; t++)
                                  ^
kmean_function.cpp: In function 'SEXPREC* distance_matrix(SEXP, SEXP, SEXP, SEXP, SEXP)':
kmean_function.cpp:211:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int i =0 ; i<num_data; i++){
                                   ^
kmean_function.cpp:217:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (unsigned int t =0 ; t < num_points; t++)
                                        ^
kmean_function.cpp: In function 'void kma_discrete(std::vector<peak>&, const int&, std::vector<int>&, const double&, const double&, const int&, const char&, const double&, const double&, std::vector<int>&, std::vector<double>&, std::vector<int>&, const double&, const double&, int, char, char)':
kmean_function.cpp:639:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while( iter < iter_max and number_distances_low < dati.size()  and cluster_vuoti==0){  //and number_clusters_different > 0
                                                   ^
kmean_function.cpp:678:52: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
       if ( (unsigned int)number_clusters_different == dati.size() & iter != 1)
                                                    ^
kmean_function.cpp:682:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (number_distances_low== dati.size())
                               ^
kmean_function.cpp: In function 'void normalize_data(std::vector<int>&, std::vector<int>&, const int&)':
kmean_function.cpp:760:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int i=0; i<n_clust; i++)
                           ^
In file included from kmean_function.cpp:1:0:
peak.h: In function 'void distance_L2_union(const peak&, const peak&, const double&, const double&, std::vector<double>&, int, char)':
peak.h:184:38: warning: 'D' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 area_def[0] = area[0]/D;
                                      ^
peak.h:130:17: note: 'D' was declared here
             int D;
                 ^
peak.h: In function 'void distance_L2_intersected(const peak&, const peak&, std::vector<double>&, int, char)':
peak.h:184:38: warning: 'D' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 area_def[0] = area[0]/D;
                                      ^
peak.h:130:17: note: 'D' was declared here
             int D;
                 ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o FunChIP.dll tmp.def kmean_function.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/FunChIP.buildbin-libdir/FunChIP/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FunChIP' as FunChIP_0.99.3.zip
* DONE (FunChIP)

FunChIP.Rcheck/examples_i386/FunChIP-Ex.timings:

nameusersystemelapsed
GR1000.080.010.09
choose_k-method0.000.020.02
cluster_peak-method3.460.003.46
compute_fragments_length4.460.064.54
distance_peak0.000.020.02
peaks0.000.010.01
pileup_peak-method0.680.070.74
plot_peak-method0.070.000.07
smooth_peak-method2.220.063.11
summit_peak-method0.010.000.01

FunChIP.Rcheck/examples_x64/FunChIP-Ex.timings:

nameusersystemelapsed
GR1000.090.010.11
choose_k-method0.030.000.03
cluster_peak-method2.760.022.78
compute_fragments_length4.240.044.43
distance_peak000
peaks0.020.000.01
pileup_peak-method0.690.030.72
plot_peak-method0.040.020.06
smooth_peak-method2.060.092.15
summit_peak-method0.000.020.01