Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-16 11:52:08 -0400 (Tue, 16 Apr 2019).
Package 562/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
FunChIP 1.8.0 Alice Parodi
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: FunChIP |
Version: 1.8.0 |
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:FunChIP.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings FunChIP_1.8.0.tar.gz |
StartedAt: 2019-04-16 00:00:47 -0400 (Tue, 16 Apr 2019) |
EndedAt: 2019-04-16 00:03:59 -0400 (Tue, 16 Apr 2019) |
EllapsedTime: 192.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: FunChIP.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:FunChIP.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings FunChIP_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/FunChIP.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FunChIP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FunChIP’ version ‘1.8.0’ * 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 ‘FunChIP’ can be installed ... WARNING Found the following significant warnings: kmean_function.cpp:677:52: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] See ‘/home/biocbuild/bbs-3.8-bioc/meat/FunChIP.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 23.6Mb sub-directories of 1Mb or more: extdata 21.5Mb libs 1.2Mb * 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 ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress peaks.rda 638Kb 112Kb xz * 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 * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed smooth_peak-method 5.728 0.18 5.915 * 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: 2 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.8-bioc/meat/FunChIP.Rcheck/00check.log’ for details.
FunChIP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL FunChIP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘FunChIP’ ... ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -fpic -g -O2 -Wall -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:74:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (unsigned int i =0 ; i<num_data; i++){ ^ kmean_function.cpp:80:34: 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:210:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (unsigned int i =0 ; i<num_data; i++){ ^ kmean_function.cpp:216:40: 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:638:51: 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:677:52: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] if ( (unsigned int)number_clusters_different == dati.size() & iter != 1) ^ kmean_function.cpp:681:31: 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:759:27: 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 member function ‘std::vector<double> peak::area(int, char) const’: peak.h:184:38: warning: ‘D’ may be used uninitialized in this function [-Wmaybe-uninitialized] area_def[0] = area[0]/D; ^ g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o FunChIP.so kmean_function.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.8-bioc/R/library/FunChIP/libs ** R ** data *** moving datasets to lazyload DB ** 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 (FunChIP)
FunChIP.Rcheck/FunChIP-Ex.timings
name | user | system | elapsed | |
GR100 | 0.044 | 0.008 | 0.053 | |
bending_index | 0.012 | 0.000 | 0.011 | |
choose_k-method | 0.112 | 0.016 | 0.127 | |
cluster_peak-method | 3.636 | 0.016 | 3.658 | |
compute_fragments_length | 3.836 | 0.076 | 4.096 | |
distance_peak | 0.008 | 0.004 | 0.010 | |
peaks | 0.004 | 0.000 | 0.002 | |
pileup_peak-method | 1.368 | 0.380 | 1.770 | |
plot_peak-method | 0.044 | 0.004 | 0.048 | |
silhouette_plot | 1.444 | 0.000 | 1.446 | |
smooth_peak-method | 5.728 | 0.180 | 5.915 | |
summit_peak-method | 0.008 | 0.000 | 0.010 | |