Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:44 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for Rbec on nebbiolo1


To the developers/maintainers of the Rbec package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbec.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1574/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rbec 1.4.0  (landing page)
Pengfan Zhang
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/Rbec
git_branch: RELEASE_3_15
git_last_commit: 4728ade
git_last_commit_date: 2022-04-26 12:15:13 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rbec
Version: 1.4.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Rbec.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Rbec_1.4.0.tar.gz
StartedAt: 2022-10-18 21:22:13 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 21:25:45 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 211.7 seconds
RetCode: 0
Status:   OK  
CheckDir: Rbec.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Rbec.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Rbec_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/Rbec.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rbec/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rbec’ version ‘1.4.0’
* 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 ‘Rbec’ can be installed ... OK
* checking installed package size ... OK
* 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 line endings in C/C++/Fortran sources/headers ... 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
Rbec 25.468  0.448  25.878
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/Rbec.Rcheck/00check.log’
for details.



Installation output

Rbec.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL Rbec
###
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##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘Rbec’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/Rbec.h:7,
                 from RcppExports.cpp:4:
../inst/include/Rbec_RcppExports.h:14:14: warning: ‘void Rbec::{anonymous}::validateSignature(const char*)’ defined but not used [-Wunused-function]
   14 |         void validateSignature(const char* sig) {
      |              ^~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c kmer_dist.cpp -o kmer_dist.o
kmer_dist.cpp: In function ‘Rcpp::NumericVector kmer_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)’:
kmer_dist.cpp:33:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   33 |   for(int i=0;i<nseqs;i++) {
      |               ~^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rcpp_test.cpp -o rcpp_test.o
rcpp_test.cpp: In function ‘void assign_kmer(uint16_t*, const char*, int)’:
rcpp_test.cpp:71:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |   if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      |      ~~^~~~~~
rcpp_test.cpp:81:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   81 |   for(i=0; i<klen; i++) {
      |            ~^~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o Rbec.so RcppExports.o kmer_dist.o rcpp_test.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Rbec/00new/Rbec/libs
** R
** 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 (Rbec)

Tests output


Example timings

Rbec.Rcheck/Rbec-Ex.timings

nameusersystemelapsed
Contam_detect0.4690.0490.527
Rbec25.468 0.44825.878