Failed to install on Ubuntu

Question

Failed to install on Ubuntu

Closed this issue 7 years ago · 8 comments

Hi,

I try to install FLXSA on Ubuntu:
/usr/lib/R/etc/Makeconf:168: recipe for target 'fl__vpa.o' failed
make: *** [fl__vpa.o] Error 1
ERROR: compilation failed for package ‘FLXSA’

removing ‘/home/george/R/x86_64-pc-linux-gnu-library/3.4/FLXSA’
Warning in install.packages :
installation of package ‘/home/george/Downloads/FLXSA_2.5.tar.gz’ had non-zero exit status

Maybe do you have any idea.

Cheers !
George

Answer 1 · 2017-12-08T09:59:50.000Z

Is this from the repository or from github?

I have Ubuntu 16.04 and either option install fine, with just some warnings about char to const conversion.

Can you try

devtools::install_github('flr/FLXSA')

Answer 2 · 2017-12-08T10:28:28.000Z

devtools::install_github('flr/FLXSA')

Downloading GitHub repo flr/FLXSA@master from URL https://api.github.com/repos/flr/FLXSA/zipball/master Installing FLXSA '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/tmp/Rtmpx4Wjp8/devtools12892c48aa71/flr-FLXSA-e832f9a' \ --library='/home/george/R/x86_64-pc-linux-gnu-library/3.4' --install-tests * installing *source* package ‘FLXSA’ ... ** libs g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fl__ctc.cpp -o fl__ctc.o g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fl__r.cpp -o fl__r.o g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fl__tun.cpp -o fl__tun.o g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fl__vpa.cpp -o fl__vpa.o fl__vpa.cpp: In member function ‘void VirtualPopAnalysis::SetRange(LPSHORT, LPSHORT, short int)’: fl__vpa.cpp:61:25: error: ‘min’ was not declared in this scope MinAge = (short)min(MinAge, Age[i]); ^~~ fl__vpa.cpp:61:25: note: suggested alternative: ‘sin’ MinAge = (short)min(MinAge, Age[i]); ^~~ sin fl__vpa.cpp:62:25: error: ‘max’ was not declared in this scope MaxAge = (short)max(MaxAge, Age[i]); ^~~ fl__vpa.cpp:62:25: note: suggested alternative: ‘fmax’ MaxAge = (short)max(MaxAge, Age[i]); ^~~ fmax fl__vpa.cpp: In member function ‘void VirtualPopAnalysis::CheckRangeWithCatch(short int)’: fl__vpa.cpp:78:14: error: ‘max’ was not declared in this scope MinAge = max(MinAge, pCatch->GetMinAge()); ^~~ fl__vpa.cpp:78:14: note: suggested alternative: ‘fmax’ MinAge = max(MinAge, pCatch->GetMinAge()); ^~~ fmax fl__vpa.cpp:80:17: error: ‘min’ was not declared in this scope MaxAge = min(pCatch->GetMaxAge(),PlusGroup-1); ^~~ fl__vpa.cpp:80:17: note: suggested alternative: ‘sin’ MaxAge = min(pCatch->GetMaxAge(),PlusGroup-1); ^~~ sin fl__vpa.cpp:82:14: error: ‘min’ was not declared in this scope MaxYear = min(MaxYear, pCatch->GetMaxYear()); ^~~ fl__vpa.cpp:82:14: note: suggested alternative: ‘sin’ MaxYear = min(MaxYear, pCatch->GetMaxYear()); ^~~ sin fl__vpa.cpp: In member function ‘void VirtualPopAnalysis::SetM(short int, double)’: fl__vpa.cpp:88:20: error: ‘max’ was not declared in this scope M[min(MaxAge,max(MinAge,iAge))][iYear] = Value; ^~~ fl__vpa.cpp:88:20: note: suggested alternative: ‘fmax’ M[min(MaxAge,max(MinAge,iAge))][iYear] = Value; ^~~ fmax fl__vpa.cpp:88:9: error: ‘min’ was not declared in this scope M[min(MaxAge,max(MinAge,iAge))][iYear] = Value; ^~~ fl__vpa.cpp:88:9: note: suggested alternative: ‘sin’ M[min(MaxAge,max(MinAge,iAge))][iYear] = Value; ^~~ sin fl__vpa.cpp: In member function ‘void VirtualPopAnalysis::SetM(short int, short int, double)’: fl__vpa.cpp:93:17: error: ‘max’ was not declared in this scope M[min(MaxAge,max(MinAge,iAge))][min(MaxYear,max(MinYear,iYear))] = Value; ^~~ fl__vpa.cpp:93:17: note: suggested alternative: ‘fmax’ M[min(MaxAge,max(MinAge,iAge))][min(MaxYear,max(MinYear,iYear))] = Value; ^~~ fmax fl__vpa.cpp:93:6: error: ‘min’ was not declared in this scope M[min(MaxAge,max(MinAge,iAge))][min(MaxYear,max(MinYear,iYear))] = Value; ^~~ fl__vpa.cpp:93:6: note: suggested alternative: ‘sin’ M[min(MaxAge,max(MinAge,iAge))][min(MaxYear,max(MinYear,iYear))] = Value; ^~~ sin fl__vpa.cpp: In member function ‘void VirtualPopAnalysis::SetF(short int, short int, double)’: fl__vpa.cpp:98:17: error: ‘max’ was not declared in this scope F[min(MaxAge,max(MinAge,iAge))][min(MaxYear,max(MinYear,iYear))] = Value; ^~~ fl__vpa.cpp:98:17: note: suggested alternative: ‘fmax’ F[min(MaxAge,max(MinAge,iAge))][min(MaxYear,max(MinYear,iYear))] = Value; ^~~ fmax fl__vpa.cpp:98:6: error: ‘min’ was not declared in this scope F[min(MaxAge,max(MinAge,iAge))][min(MaxYear,max(MinYear,iYear))] = Value; ^~~ fl__vpa.cpp:98:6: note: suggested alternative: ‘sin’ F[min(MaxAge,max(MinAge,iAge))][min(MaxYear,max(MinYear,iYear))] = Value; ^~~ sin fl__vpa.cpp: In member function ‘double VirtualPopAnalysis::GetN(short int, short int)’: fl__vpa.cpp:148:11: error: ‘max’ was not declared in this scope return max(0.0,N[iAge][iYear]); ^~~ fl__vpa.cpp:148:11: note: suggested alternative: ‘fmax’ return max(0.0,N[iAge][iYear]); ^~~ fmax fl__vpa.cpp: In member function ‘double VirtualPopAnalysis::GetF(short int, short int)’: fl__vpa.cpp:153:25: error: ‘max’ was not declared in this scope return max(0.0,F[min(max(iAge,MinAge),MaxAge)][min(max(iYear,MinYear),MaxYear)]); ^~~ fl__vpa.cpp:153:25: note: suggested alternative: ‘fmax’ return max(0.0,F[min(max(iAge,MinAge),MaxAge)][min(max(iYear,MinYear),MaxYear)]); ^~~ fmax fl__vpa.cpp:153:21: error: ‘min’ was not declared in this scope return max(0.0,F[min(max(iAge,MinAge),MaxAge)][min(max(iYear,MinYear),MaxYear)]); ^~~ fl__vpa.cpp:153:21: note: suggested alternative: ‘sin’ return max(0.0,F[min(max(iAge,MinAge),MaxAge)][min(max(iYear,MinYear),MaxYear)]); ^~~ sin fl__vpa.cpp:153:11: error: ‘max’ was not declared in this scope return max(0.0,F[min(max(iAge,MinAge),MaxAge)][min(max(iYear,MinYear),MaxYear)]); ^~~ fl__vpa.cpp:153:11: note: suggested alternative: ‘fmax’ return max(0.0,F[min(max(iAge,MinAge),MaxAge)][min(max(iYear,MinYear),MaxYear)]); ^~~ fmax fl__vpa.cpp: In member function ‘double VirtualPopAnalysis::GetM(short int)’: fl__vpa.cpp:158:25: error: ‘max’ was not declared in this scope return max(0.0,M[min(max(iAge,MinAge),MaxAge)][MinYear]); ^~~ fl__vpa.cpp:158:25: note: suggested alternative: ‘fmax’ return max(0.0,M[min(max(iAge,MinAge),MaxAge)][MinYear]); ^~~ fmax fl__vpa.cpp:158:21: error: ‘min’ was not declared in this scope return max(0.0,M[min(max(iAge,MinAge),MaxAge)][MinYear]); ^~~ fl__vpa.cpp:158:21: note: suggested alternative: ‘sin’ return max(0.0,M[min(max(iAge,MinAge),MaxAge)][MinYear]); ^~~ sin fl__vpa.cpp:158:11: error: ‘max’ was not declared in this scope return max(0.0,M[min(max(iAge,MinAge),MaxAge)][MinYear]); ^~~ fl__vpa.cpp:158:11: note: suggested alternative: ‘fmax’ return max(0.0,M[min(max(iAge,MinAge),MaxAge)][MinYear]); ^~~ fmax fl__vpa.cpp: In member function ‘double VirtualPopAnalysis::GetM(short int, short int)’: fl__vpa.cpp:163:25: error: ‘max’ was not declared in this scope return max(0.0,M[min(max(iAge,MinAge),MaxAge)][min(max(iYear,MinYear),MaxYear)]); ^~~ fl__vpa.cpp:163:25: note: suggested alternative: ‘fmax’ return max(0.0,M[min(max(iAge,MinAge),MaxAge)][min(max(iYear,MinYear),MaxYear)]); ^~~ fmax fl__vpa.cpp:163:21: error: ‘min’ was not declared in this scope return max(0.0,M[min(max(iAge,MinAge),MaxAge)][min(max(iYear,MinYear),MaxYear)]); ^~~ fl__vpa.cpp:163:21: note: suggested alternative: ‘sin’ return max(0.0,M[min(max(iAge,MinAge),MaxAge)][min(max(iYear,MinYear),MaxYear)]); ^~~ sin fl__vpa.cpp:163:11: error: ‘max’ was not declared in this scope return max(0.0,M[min(max(iAge,MinAge),MaxAge)][min(max(iYear,MinYear),MaxYear)]); ^~~ fl__vpa.cpp:163:11: note: suggested alternative: ‘fmax’ return max(0.0,M[min(max(iAge,MinAge),MaxAge)][min(max(iYear,MinYear),MaxYear)]); ^~~ fmax fl__vpa.cpp: In member function ‘bool VirtualPopAnalysis::RunCohortAnalysis()’: fl__vpa.cpp:171:20: error: ‘min’ was not declared in this scope for (iAge = min(MaxAge, MaxYear - iYearClass); iAge >= max(MinAge, MinYear - iYearClass); iAge--) ^~~ fl__vpa.cpp:171:20: note: suggested alternative: ‘sin’ for (iAge = min(MaxAge, MaxYear - iYearClass); iAge >= max(MinAge, MinYear - iYearClass); iAge--) ^~~ sin fl__vpa.cpp:171:63: error: ‘max’ was not declared in this scope for (iAge = min(MaxAge, MaxYear - iYearClass); iAge >= max(MinAge, MinYear - iYearClass); iAge--) ^~~ fl__vpa.cpp:171:63: note: suggested alternative: ‘fmax’ for (iAge = min(MaxAge, MaxYear - iYearClass); iAge >= max(MinAge, MinYear - iYearClass); iAge--) ^~~ fmax fl__vpa.cpp: In member function ‘bool VirtualPopAnalysis::RunVPA()’: fl__vpa.cpp:205:19: error: ‘min’ was not declared in this scope for (iAge = min(MaxAge, MaxYear - iYearClass); iAge >= max(MinAge, MinYear - iYearClass); iAge--) ^~~ fl__vpa.cpp:205:19: note: suggested alternative: ‘sin’ for (iAge = min(MaxAge, MaxYear - iYearClass); iAge >= max(MinAge, MinYear - iYearClass); iAge--) ^~~ sin fl__vpa.cpp:205:62: error: ‘max’ was not declared in this scope for (iAge = min(MaxAge, MaxYear - iYearClass); iAge >= max(MinAge, MinYear - iYearClass); iAge--) ^~~ fl__vpa.cpp:205:62: note: suggested alternative: ‘fmax’ for (iAge = min(MaxAge, MaxYear - iYearClass); iAge >= max(MinAge, MinYear - iYearClass); iAge--) ^~~ fmax /usr/lib/R/etc/Makeconf:168: recipe for target 'fl__vpa.o' failed make: *** [fl__vpa.o] Error 1 ERROR: compilation failed for package ‘FLXSA’ * removing ‘/home/george/R/x86_64-pc-linux-gnu-library/3.4/FLXSA’ Installation failed: Command failed (1) 2017-12-08 4:59 GMT-05:00 Iago Mosqueira <notifications@github.com>:

…

Is this from the repository or from github? I have Ubuntu 16.04 and either option install fine, with just some warnings about char to const conversion. Can you try devtools::install_github('flr/FLXSA') — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APeMa7XGAWpaVNktdJ6EizoNuLPBB8f_ks5s-QiWgaJpZM4Q6vnV> .

Answer 3 · 2017-12-08T10:59:52.000Z

Can you tell me what version of gcc are you using?

gcc -v gives me, at the end of the output

gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.5)

Answer 4 · 2017-12-08T11:03:02.000Z

Ubuntu 17.10 gcc version 7.2.0 (Ubuntu 7.2.0-8ubuntu3) 2017-12-08 5:59 GMT-05:00 Iago Mosqueira <notifications@github.com>:

…

Can you tell me what version of gcc are you using? gcc -v gives me, at the end of the output gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.5) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APeMa8dMTlir_Vb7TJ8_8AJoQOH0YXWBks5s-RapgaJpZM4Q6vnV> .

Answer 5 · 2017-12-08T11:11:57.000Z

OK, I will have to setup a virtual system to test this. I assume some new checks in newer ggc versions are failing on the old codebase of FLXSA. I will get back to you as soon as I am able to devote some time to this.

Answer 6 · 2017-12-08T11:22:24.000Z

OK, great...many thanks ! Looking forward to your reply. 2017-12-08 6:11 GMT-05:00 Iago Mosqueira <notifications@github.com>:

…

OK, I will have to setup a virtual system to test this. I assume some new checks in newer ggc versions are failing on the old codebase of FLXSA. I will get back to you as soon as I am able to devote some time to this. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APeMa8GOvBrI-6zViY0SRWMkcgCQgOERks5s-Rl9gaJpZM4Q6vnV> .

Answer 7 · 2017-12-12T13:51:52.000Z

Some changes to the definition of min and max appear to solve the problem. These changes bring other problems in gvv 4.8.4, so I am committing these changes under the gcc720 branch, for the time being

https://github.com/flr/FLXSA/tree/gcc720

I have not tested the results too much yet, any feedback more that welcome.

You can install using

devtools::install_github('flr/FLXSA', ref='gcc720')

Answer 8 · 2017-12-12T14:51:26.000Z

Found a better fix, changing min/max to use std::min/max and the newer malloc. Some type casting along the way, as short gets changed to int if 1 is substracted.

So master branch appears to work now on both versions of gcc. Try with

devtools::install_github('flr/FLXSA')