Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2022-04-13 12:05:42 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 NuPoP on nebbiolo2


To the developers/maintainers of the NuPoP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/NuPoP.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 1311/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NuPoP 2.2.0  (landing page)
Ji-Ping Wang
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/NuPoP
git_branch: RELEASE_3_14
git_last_commit: ab10a61
git_last_commit_date: 2021-10-26 11:56:48 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NuPoP
Version: 2.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NuPoP.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NuPoP_2.2.0.tar.gz
StartedAt: 2022-04-12 08:30:41 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:31:07 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 26.3 seconds
RetCode: 0
Status:   OK  
CheckDir: NuPoP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NuPoP.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NuPoP_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/NuPoP.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NuPoP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NuPoP’ version ‘2.2.0’
* 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 ‘NuPoP’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R         3.3Mb
    doc       1.3Mb
    extdata   2.2Mb
* 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 R/sysdata.rda ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  sysdata.rda    4.6Mb    2.9Mb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.14-bioc/R/library/NuPoP/libs/NuPoP.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)

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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/NuPoP.Rcheck/00check.log’
for details.



Installation output

NuPoP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL NuPoP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘NuPoP’ ...
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -c  vtbfb.f90 -o vtbfb.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -c  vtbfbNL4.f90 -o vtbfbNL4.o
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o NuPoP.so vtbfb.o vtbfbNL4.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-NuPoP/00new/NuPoP/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘NuPoP.Rmd’ using ‘UTF-8’ 
** 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 (NuPoP)

Tests output


Example timings

NuPoP.Rcheck/NuPoP-Ex.timings

nameusersystemelapsed
NuPoP-package1.6740.0281.702
plotNuPoP0.0570.0000.057
predNuPoP1.5810.0121.594
predNuPoP_chem1.6300.0081.638
readNuPoP1.6090.0001.609