Hi, sorry here is the complete code I did with the error message:
library(devtools)
Loading required package: usethis
devtools::install_github("BaderLab/HumanLiver")
Downloading GitHub repo BaderLab/HumanLiver@master
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: ps (1.3.2 -> 1.3.3 ) [CRAN]
5: lsei (1.2-0 -> 1.2-0.1) [CRAN]
Enter one or more numbers, or an empty line to skip updates:
3
✓ checking for file ‘/private/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T/RtmpgQdFfA/remotesbbd2a1e9ca1/BaderLab-HumanLiver-39c873b/DESCRIPTION’ ...
─ preparing ‘HumanLiver’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: ‘HumanLiver/inst/liver/HumanLiver.RData’
─ building ‘HumanLiver_1.5.0.tar.gz’
- installing source package ‘HumanLiver’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
sh: line 1: 3085 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T//Rtmpie9mbp/filec06653d2759'
ERROR: lazy loading failed for package ‘HumanLiver’
- removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/HumanLiver’
installation of package ‘/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T//RtmpgQdFfA/filebbd3fbd23a1/HumanLiver_1.5.0.tar.gz’ had non-zero exit status
This is what happens when I choose the option 3 for update. As you can see I can choose to update all packages (1), CRAN only (2), None (3), ps (4) or lsei (5). I tried all options but nothing seems to work, I believe it is because I fail to update "lsei" (option 5). When I try option 5 here is what I get:
devtools::install_github("BaderLab/HumanLiver")
Downloading GitHub repo BaderLab/HumanLiver@master
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: ps (1.3.2 -> 1.3.3 ) [CRAN]
5: lsei (1.2-0 -> 1.2-0.1) [CRAN]
Enter one or more numbers, or an empty line to skip updates:
5
lsei (1.2-0 -> 1.2-0.1) [CRAN]
Installing 1 packages: lsei
There is a binary version available but the source version is later:
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/lsei_1.2-0.tgz'
Content type 'application/x-gzip' length 80866 bytes (78 KB)
downloaded 78 KB
The downloaded binary packages are in
/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T//RtmpgQdFfA/downloaded_packages
✓ checking for file ‘/private/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T/RtmpgQdFfA/remotesbbd629bf07/BaderLab-HumanLiver-39c873b/DESCRIPTION’ ...
─ preparing ‘HumanLiver’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: ‘HumanLiver/inst/liver/HumanLiver.RData’
─ building ‘HumanLiver_1.5.0.tar.gz’
- installing source package ‘HumanLiver’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
sh: line 1: 3131 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T//Rtmp9JxezF/filec341c5f6c7c'
ERROR: lazy loading failed for package ‘HumanLiver’
- removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/HumanLiver’
installation of package ‘/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T//RtmpgQdFfA/filebbd20944d53/HumanLiver_1.5.0.tar.gz’ had non-zero exit status
So again I have the choice between Yes and No for the compilation of "lsei", if I choose no my next command fails because the installation of the package I need from github seems to need the updated "lsei". And if I choose Yes, I have the folowwing message:
installing source package ‘lsei’ ...
** package ‘lsei’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c lsei.f -o lsei.o
*ake: gfortran: No such file or directory
make: *** [lsei.o] Error 1
ERROR: compilation failed for package ‘lsei’
removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/lsei’
Warning in install.packages :
installation of package ‘lsei’ had non-zero exit status
ERROR: dependency ‘lsei’ is not available for package ‘npsurv’
removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/npsurv’
Warning in install.packages :
installation of package ‘npsurv’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T/RtmpwlqTAv/downloaded_packages’