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INSTALL report for rGADEM on taxco

This page was generated on 2021-01-31 03:53:36 -0500 (Sun, 31 Jan 2021).

These are experimental builds on Apple's new arm64 arch. See here for more information.
To the developers/maintainers of the rGADEM package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1480/1938HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rGADEM 2.39.0
Arnaud Droit
Snapshot Date: 2021-01-30 14:40:03 -0500 (Sat, 30 Jan 2021)
URL: https://git.bioconductor.org/packages/rGADEM
Branch: master
Last Commit: 0998134
Last Changed Date: 2020-10-27 10:37:29 -0500 (Tue, 27 Oct 2020)
taxcomacOS 11.0.1 Big Sur / arm64  ERROR    NA    NA  

Summary

Package: rGADEM
Version: 2.39.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rGADEM
StartedAt: 2021-01-30 17:48:22 -0500 (Sat, 30 Jan 2021)
EndedAt: 2021-01-30 17:48:52 -0500 (Sat, 30 Jan 2021)
EllapsedTime: 30.2 seconds
RetCode: 1
Status:   ERROR  

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rGADEM
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library’
* installing *source* package ‘rGADEM’ ...
** using staged installation
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for clang option to support OpenMP... unsupported
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dispatch/dispatch.h usability... yes
checking dispatch/dispatch.h presence... yes
checking for dispatch/dispatch.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
config.status: src/config.h is unchanged
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c Gadem_Analysis.c -o Gadem_Analysis.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c align_sites.c -o align_sites.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c alloc.c -o alloc.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c background.c -o background.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c base_frequency.c -o base_frequency.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c check_convergence.c -o check_convergence.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c check_pwm_dist.c -o check_pwm_dist.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c consensus.c -o consensus.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c construct_pwm.c -o construct_pwm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c copy_pwm.c -o copy_pwm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c crossover.c -o crossover.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c effect_seq_len.c -o effect_seq_len.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c evalue_meme.c -o evalue_meme.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c extend_alignment.c -o extend_alignment.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c initial_population.c -o initial_population.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c mask_sites.c -o mask_sites.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c mutation.c -o mutation.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c normalization.c -o normalization.o
normalization.c:124:13: error: implicit declaration of function 'Rprintf' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
  if(i==20) Rprintf("score is smaller than 10e-20\n");
            ^
1 error generated.
make: *** [normalization.o] Error 1
ERROR: compilation failed for package ‘rGADEM’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/rGADEM’