Alice Parodi
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/FunChIP |
| Branch: RELEASE_3_11 |
| Last Commit: e324589 |
| Last Changed Date: 2020-04-27 14:58:01 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:54:46 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE FunChIP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 643/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| FunChIP 1.14.0 Alice Parodi
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: FunChIP |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:FunChIP.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings FunChIP_1.14.0.tar.gz |
| StartedAt: 2020-10-17 01:27:11 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 01:30:37 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 206.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: FunChIP.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:FunChIP.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings FunChIP_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/FunChIP.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.14.0’
* 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-3.11-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 1.3Mb
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
smooth_peak-method 5.078 0.12 5.199
* 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-3.11-bioc/meat/FunChIP.Rcheck/00check.log’
for details.
FunChIP.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL FunChIP
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘FunChIP’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include `/home/biocbuild/bbs-3.11-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:154:46: warning: ‘D’ may be used uninitialized in this function [-Wmaybe-uninitialized]
area_def[0] = sqrt(area[0]/2)/D;
~~~~~~~~~~~~~~~^~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o FunChIP.so kmean_function.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-FunChIP/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FunChIP)
FunChIP.Rcheck/FunChIP-Ex.timings
| name | user | system | elapsed | |
| GR100 | 0.092 | 0.004 | 0.096 | |
| bending_index | 0.019 | 0.005 | 0.025 | |
| choose_k-method | 0.101 | 0.012 | 0.113 | |
| cluster_peak-method | 2.309 | 0.000 | 2.309 | |
| compute_fragments_length | 3.979 | 0.115 | 4.355 | |
| distance_peak | 0.015 | 0.000 | 0.016 | |
| peaks | 0.001 | 0.000 | 0.001 | |
| pileup_peak-method | 2.976 | 0.532 | 3.523 | |
| plot_peak-method | 0.091 | 0.004 | 0.094 | |
| silhouette_plot | 1.929 | 0.032 | 1.962 | |
| smooth_peak-method | 5.078 | 0.120 | 5.199 | |
| summit_peak-method | 0.013 | 0.000 | 0.013 | |