Multiple platform build/check report for BioC 3.20 - INSTALL results for VegaMC on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 VegaMC on kjohnson1

To the developers/maintainers of the VegaMC package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VegaMC.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: VegaMC

Version: 3.44.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VegaMC

StartedAt: 2024-12-19 16:25:38 -0500 (Thu, 19 Dec 2024)

EndedAt: 2024-12-19 16:25:56 -0500 (Thu, 19 Dec 2024)

EllapsedTime: 18.0 seconds

RetCode: 0

Status: OK

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VegaMC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘VegaMC’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c run_vegaMC.c -o run_vegaMC.o
run_vegaMC.c:144:62: warning: data argument not used by format string [-Wformat-extra-args]
    Rprintf("\tAberration Matrices Successfully Computed\n", num_seg_regions);
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ^
run_vegaMC.c:150:13: warning: data argument not used by format string [-Wformat-extra-args]
            num_seg_regions);
            ^
run_vegaMC.c:317:17: warning: variable 'tot_baf' set but not used [-Wunused-but-set-variable]
            int tot_baf = 0;
                ^
run_vegaMC.c:491:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^~~~
run_vegaMC.c:526:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^~~~
run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable]
    char *elem, *brkt;
                 ^
6 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sort_data.c -o sort_data.o
sort_data.c:131:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^~~~
sort_data.c:180:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^~~~
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vegaMC.c -o vegaMC.o
vegaMC.c:235:10: warning: variable 'deleted' set but not used [-Wunused-but-set-variable]
    node deleted;
         ^
vegaMC.c:458:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    lambda_gradient = abs(lambda);
                      ^
vegaMC.c:458:23: note: use function 'fabsf' instead
    lambda_gradient = abs(lambda);
                      ^~~
                      fabsf
vegaMC.c:592:15: warning: variable 'index' set but not used [-Wunused-but-set-variable]
    int i, j, index;
              ^
3 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o VegaMC.so run_vegaMC.o sort_data.o vegaMC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-VegaMC/00new/VegaMC/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 (VegaMC)