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This page was generated on 2022-06-27 11:09:59 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 makecdfenv on nebbiolo1


To the developers/maintainers of the makecdfenv package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/makecdfenv.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 1067/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
makecdfenv 1.72.0  (landing page)
James W. MacDonald
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/makecdfenv
git_branch: RELEASE_3_15
git_last_commit: 85c8968
git_last_commit_date: 2022-04-26 10:54:49 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: makecdfenv
Version: 1.72.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:makecdfenv.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings makecdfenv_1.72.0.tar.gz
StartedAt: 2022-06-26 20:30:59 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 20:31:32 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 33.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: makecdfenv.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:makecdfenv.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings makecdfenv_1.72.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/makecdfenv.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘makecdfenv/DESCRIPTION’ ... OK
* this is package ‘makecdfenv’ version ‘1.72.0’
* 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 ‘makecdfenv’ can be installed ... WARNING
Found the following significant warnings:
  read_cdffile.c:340:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/biocbuild/bbs-3.15-bioc/meat/makecdfenv.Rcheck/00install.out’ for details.
* 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 ... NOTE
Foreign function calls to a different package:
  .Call("CheckCDFXDA", ..., PACKAGE = "affyio")
  .Call("ReadCDFFile", ..., PACKAGE = "affyio")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* 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
* 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 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/makecdfenv.Rcheck/00check.log’
for details.



Installation output

makecdfenv.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL makecdfenv
###
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘makecdfenv’ ...
** using staged installation
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include   -fpic  -g -O2  -Wall -c read_cdffile.c -o read_cdffile.o
read_cdffile.c: In function ‘readQC’:
read_cdffile.c:576:7: warning: variable ‘typeQC’ set but not used [-Wunused-but-set-variable]
  576 |   int typeQC;
      |       ^~~~~~
read_cdffile.c: In function ‘openCDFfile’:
read_cdffile.c:340:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  340 |       fgets(buffy, SIZE_LINE, affyFile->stream);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o makecdfenv.so read_cdffile.o -lz -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-makecdfenv/00new/makecdfenv/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 (makecdfenv)

Tests output


Example timings

makecdfenv.Rcheck/makecdfenv-Ex.timings

nameusersystemelapsed
make.cdf.env2.3870.0732.460
make.cdf.package2.5860.0702.658
read.cdffile2.1420.0292.170