Alice Parodi
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/FunChIP |
| git_branch: RELEASE_3_13 |
| git_last_commit: 4981a2b |
| git_last_commit_date: 2021-05-19 12:20:50 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:05 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the FunChIP package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FunChIP.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 680/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FunChIP 1.18.0 (landing page) Alice Parodi
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FunChIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings FunChIP_1.18.0.tar.gz |
| StartedAt: 2021-10-14 23:20:37 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:25:17 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 280.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: FunChIP.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FunChIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings FunChIP_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/FunChIP.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.18.0'
* 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 '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 'C:/Users/biocbuild/bbs-3.13-bioc/meat/FunChIP.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 24.5Mb
sub-directories of 1Mb or more:
extdata 21.5Mb
libs 2.1Mb
* 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
* 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 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 LazyData ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/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)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/FunChIP/libs/x64/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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
smooth_peak-method 4.46 0.89 5.36
** running examples for arch 'x64' ... 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: 2 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/FunChIP.Rcheck/00check.log'
for details.
FunChIP.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/FunChIP_1.18.0.tar.gz && rm -rf FunChIP.buildbin-libdir && mkdir FunChIP.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FunChIP.buildbin-libdir FunChIP_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL FunChIP_1.18.0.zip && rm FunChIP_1.18.0.tar.gz FunChIP_1.18.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
4 22.0M 4 1038k 0 0 1718k 0 0:00:13 --:--:-- 0:00:13 1719k
19 22.0M 19 4492k 0 0 2773k 0 0:00:08 0:00:01 0:00:07 2773k
39 22.0M 39 8855k 0 0 3354k 0 0:00:06 0:00:02 0:00:04 3354k
60 22.0M 60 13.3M 0 0 3791k 0 0:00:05 0:00:03 0:00:02 3791k
87 22.0M 87 19.3M 0 0 4303k 0 0:00:05 0:00:04 0:00:01 4303k
100 22.0M 100 22.0M 0 0 4510k 0 0:00:05 0:00:05 --:--:-- 4894k
install for i386
* installing *source* package 'FunChIP' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I../inst/include -I. -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for (unsigned int i =0 ; i<num_data; i++){
~^~~~~~~~~
kmean_function.cpp:80:34: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-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 of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for (unsigned int i =0 ; i<num_data; i++){
~^~~~~~~~~
kmean_function.cpp:216:40: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-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 of integer expressions of different signedness: 'int' and 'std::vector<peak>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<peak>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
for (unsigned int i=0; i<n_clust; i++)
~^~~~~~~~
In file included from kmean_function.cpp:1:
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;
~~~~~~~~~~~~~~~^~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o FunChIP.dll tmp.def kmean_function.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/FunChIP.buildbin-libdir/00LOCK-FunChIP/00new/FunChIP/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'FunChIP'
finding HTML links ... done
FunChIP-package html
GR100 html
finding level-2 HTML links ... done
bending_index html
choose_k-method html
cluster_peak-method html
compute_fragments_length html
distance_peak html
peaks html
pileup_peak-method html
plot_peak-method html
silhouette_plot html
smooth_peak-method html
summit_peak-method html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'FunChIP' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I../inst/include -I. -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for (unsigned int i =0 ; i<num_data; i++){
~^~~~~~~~~
kmean_function.cpp:80:34: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-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 of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for (unsigned int i =0 ; i<num_data; i++){
~^~~~~~~~~
kmean_function.cpp:216:40: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-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 of integer expressions of different signedness: 'int' and 'std::vector<peak>::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<peak>::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
for (unsigned int i=0; i<n_clust; i++)
~^~~~~~~~
In file included from kmean_function.cpp:1:
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;
~~~~~~~~~~~~~~~^~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o FunChIP.dll tmp.def kmean_function.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/FunChIP.buildbin-libdir/FunChIP/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FunChIP' as FunChIP_1.18.0.zip
* DONE (FunChIP)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'FunChIP' successfully unpacked and MD5 sums checked
|
FunChIP.Rcheck/examples_i386/FunChIP-Ex.timings
|
FunChIP.Rcheck/examples_x64/FunChIP-Ex.timings
|