Multiple platform build/check report for BioC 3.21 - INSTALL results for makecdfenv on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4833
merida1	macOS 12.7.6 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4614
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4555
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4586
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*

INSTALL results for makecdfenv on nebbiolo1

To the developers/maintainers of the makecdfenv package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: makecdfenv

Version: 1.84.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL makecdfenv

StartedAt: 2025-10-15 15:12:17 -0400 (Wed, 15 Oct 2025)

EndedAt: 2025-10-15 15:12:22 -0400 (Wed, 15 Oct 2025)

EllapsedTime: 4.6 seconds

RetCode: 0

Status: OK

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL makecdfenv
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘makecdfenv’ ...
** this is package ‘makecdfenv’ version ‘1.84.0’
** using staged installation
creating cache ./config.cache
checking how to run the C preprocessor... gcc -std=gnu2x -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
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include   -g -O2 -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security -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 -std=gnu2x -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o makecdfenv.so read_cdffile.o -lz -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-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)