bug#42141: blast+ is not reproducible
Hi, Ricardo Wurmus writes: > zimoun writes: > >> Hi, >> >> On Thu, 29 Sep 2022 at 23:09, Maxim Cournoyer >> wrote: >>> Ricardo Wurmus writes: >>> Fixed with commit 1ee2d117d8fa9e2e0d4ec46cc497bb5e6337. >>> >>> Yay! Thank you! And for my curiosity, how did I get the two build >>> farms to agree on an identical build, as reported in 'guix challenge'? >>> >>> That is odd. >> >> Because blast+ is multi-outputs and ’out’ is fine contrary to ’include’: >> >> $ guix challenge blast+:include >> /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include contents >> differ: >> local hash: 0q4nssknlmc54m8abndn9bhrlwm4m28lkb75i1wnwr0ghbalj02x >> >> https://ci.guix.gnu.org/nar/lzip/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast%2B-2.11.0-include: >> 0q4nssknlmc54m8abndn9bhrlwm4m28lkb75i1wnwr0ghbalj02x >> >> https://bordeaux.guix.gnu.org/nar/lzip/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast%2B-2.11.0-include: >> 0cakizfsqb1lla62cmwnng1h9gvqgf3lyjk0k7lkiaisj713mpzx >> differing files: >> /include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h >> /include/ncbi-tools++/ncbi-tools++/ncbiconf_unix.h >> >> 1 store items were analyzed: >> - 0 (0.0%) were identical >> - 1 (100.0%) differed >> - 0 (0.0%) were inconclusive > > Ah, thanks for explaining! Ah! Shouldn't the default be to compare all outputs? It seems that'd be less surprising and useful. What do you think? -- Maxim
bug#42141: blast+ is not reproducible
zimoun writes: > Hi, > > On Thu, 29 Sep 2022 at 23:09, Maxim Cournoyer > wrote: >> Ricardo Wurmus writes: >> >>> Fixed with commit 1ee2d117d8fa9e2e0d4ec46cc497bb5e6337. >> >> Yay! Thank you! And for my curiosity, how did I get the two build >> farms to agree on an identical build, as reported in 'guix challenge'? >> >> That is odd. > > Because blast+ is multi-outputs and ’out’ is fine contrary to ’include’: > > $ guix challenge blast+:include > /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include contents > differ: > local hash: 0q4nssknlmc54m8abndn9bhrlwm4m28lkb75i1wnwr0ghbalj02x > > https://ci.guix.gnu.org/nar/lzip/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast%2B-2.11.0-include: > 0q4nssknlmc54m8abndn9bhrlwm4m28lkb75i1wnwr0ghbalj02x > > https://bordeaux.guix.gnu.org/nar/lzip/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast%2B-2.11.0-include: > 0cakizfsqb1lla62cmwnng1h9gvqgf3lyjk0k7lkiaisj713mpzx > differing files: > /include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h > /include/ncbi-tools++/ncbi-tools++/ncbiconf_unix.h > > 1 store items were analyzed: > - 0 (0.0%) were identical > - 1 (100.0%) differed > - 0 (0.0%) were inconclusive Ah, thanks for explaining! -- Ricardo
bug#42141: blast+ is not reproducible
Hi, On Thu, 29 Sep 2022 at 23:09, Maxim Cournoyer wrote: > Ricardo Wurmus writes: > >> Fixed with commit 1ee2d117d8fa9e2e0d4ec46cc497bb5e6337. > > Yay! Thank you! And for my curiosity, how did I get the two build > farms to agree on an identical build, as reported in 'guix challenge'? > > That is odd. Because blast+ is multi-outputs and ’out’ is fine contrary to ’include’: --8<---cut here---start->8--- $ guix challenge blast+:include /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include contents differ: local hash: 0q4nssknlmc54m8abndn9bhrlwm4m28lkb75i1wnwr0ghbalj02x https://ci.guix.gnu.org/nar/lzip/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast%2B-2.11.0-include: 0q4nssknlmc54m8abndn9bhrlwm4m28lkb75i1wnwr0ghbalj02x https://bordeaux.guix.gnu.org/nar/lzip/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast%2B-2.11.0-include: 0cakizfsqb1lla62cmwnng1h9gvqgf3lyjk0k7lkiaisj713mpzx differing files: /include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h /include/ncbi-tools++/ncbi-tools++/ncbiconf_unix.h 1 store items were analyzed: - 0 (0.0%) were identical - 1 (100.0%) differed - 0 (0.0%) were inconclusive --8<---cut here---end--->8--- Cheers, simon
bug#42141: blast+ is not reproducible
Maxim Cournoyer writes: > Ricardo Wurmus writes: > >> Fixed with commit 1ee2d117d8fa9e2e0d4ec46cc497bb5e6337. > > Yay! Thank you! And for my curiosity, how did I get the two build > farms to agree on an identical build, as reported in 'guix challenge'? > > That is odd. I don’t know. I also got the same result from “guix challenge”, but I hadn’t built it locally. It was only when I built it on my machine (and with “--check”) that I confirmed that the issue still existed. Any way of making “guix challenge” tell us more about what it actually compared? -- Ricardo
bug#42141: blast+ is not reproducible
Hello, Ricardo Wurmus writes: > Fixed with commit 1ee2d117d8fa9e2e0d4ec46cc497bb5e6337. Yay! Thank you! And for my curiosity, how did I get the two build farms to agree on an identical build, as reported in 'guix challenge'? That is odd. -- Maxim
bug#42141: blast+ is not reproducible
Fixed with commit 1ee2d117d8fa9e2e0d4ec46cc497bb5e6337. -- Ricardo
bug#42141: blast+ is not reproducible
Ricardo Wurmus writes: > reopen 42141 > thanks > > Maxim Cournoyer writes: > >> Hi, >> >> Ricardo Wurmus writes: >> >>> This should be rather easy to fix: >>> >>> diff -r >>> /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include >>> /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include-check >>> diff -r >>> /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h >>> /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include-check/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h >>> 4,13c4,13 >>> < #define NCBI_RANDOM_VALUE_01770246234u >>> < #define NCBI_RANDOM_VALUE_12685550394u >>> < #define NCBI_RANDOM_VALUE_21952513968u >>> < #define NCBI_RANDOM_VALUE_34081691487u >>> < #define NCBI_RANDOM_VALUE_41126642990u >>> < #define NCBI_RANDOM_VALUE_52363626105u >>> < #define NCBI_RANDOM_VALUE_6444644742u >>> < #define NCBI_RANDOM_VALUE_72799580837u >>> < #define NCBI_RANDOM_VALUE_8216161479u >>> < #define NCBI_RANDOM_VALUE_9992434062u >>> --- #define NCBI_RANDOM_VALUE_02851596927u #define NCBI_RANDOM_VALUE_14039058594u #define NCBI_RANDOM_VALUE_23204116600u #define NCBI_RANDOM_VALUE_34270143185u #define NCBI_RANDOM_VALUE_41366873742u #define NCBI_RANDOM_VALUE_5703144487u #define NCBI_RANDOM_VALUE_62507785646u #define NCBI_RANDOM_VALUE_73995716134u #define NCBI_RANDOM_VALUE_8907933519u #define NCBI_RANDOM_VALUE_91149060107u >> >> Not anymore, according to: >> >> $ guix challenge blast+ >> >> 1 store items were analyzed: >> - 1 (100.0%) were identical >> - 0 (0.0%) differed >> - 0 (0.0%) were inconclusive > > This is still a problem: > > $ diff -ru /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include > /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include-check > diff -ru > /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include/include/ncbi-tools++/ncbi-tools++/ncbiconf_unix.h > > /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include-check/include/ncbi-tools++/ncbi-tools++/ncbiconf_unix.h > --- > /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include/include/ncbi-tools++/ncbi-tools++/ncbiconf_unix.h >1970-01-01 01:00:01.0 +0100 > +++ > /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include-check/include/ncbi-tools++/ncbi-tools++/ncbiconf_unix.h > 1970-01-01 01:00:01.0 +0100 > @@ -1095,7 +1095,7 @@ > > /* Build signature: compiler-name '_' compiler-version '-' configuration '--' > platform-name '-' hostname */ > -#define NCBI_SIGNATURE > "GCC_1030-DebugMTDLL64--x86_64-unknown-linux5.15.10-gnu2.33-localhost" > +#define NCBI_SIGNATURE > "GCC_1030-DebugMTDLL64--x86_64-unknown-linux5.15.59-gnu2.33-localhost" > > /* Define to 1 if SQLColAttribute's last argument is an SQLLEN * */ > #define NCBI_SQLCOLATTRIBUTE_SQLLEN 1 > diff -ru > /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h > > /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include-check/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h > --- > /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h >1970-01-01 01:00:01.0 +0100 > +++ > /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include-check/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h > 1970-01-01 01:00:01.0 +0100 > @@ -1,13 +1,13 @@ > #define NCBI_RANDOM_VALUE_TYPE Uint4 > #define NCBI_RANDOM_VALUE_MIN 0 > #define NCBI_RANDOM_VALUE_MAX 0xu > -#define NCBI_RANDOM_VALUE_03249030781u > -#define NCBI_RANDOM_VALUE_13573796697u > -#define NCBI_RANDOM_VALUE_22130009325u > -#define NCBI_RANDOM_VALUE_34284761029u > -#define NCBI_RANDOM_VALUE_43467737853u > -#define NCBI_RANDOM_VALUE_53267844710u > -#define NCBI_RANDOM_VALUE_64107058373u > -#define NCBI_RANDOM_VALUE_7166436459u > -#define NCBI_RANDOM_VALUE_8960927418u > -#define NCBI_RANDOM_VALUE_93839848519u > +#define NCBI_RANDOM_VALUE_02845495105u > +#define NCBI_RANDOM_VALUE_12158634051u > +#define NCBI_RANDOM_VALUE_24072202242u > +#define NCBI_RANDOM_VALUE_3902228395u > +#define NCBI_RANDOM_VALUE_41353323915u > +#define NCBI_RANDOM_VALUE_5574823513u > +#define NCBI_RANDOM_VALUE_64119501261u > +#define NCBI_RANDOM_VALUE_72477640938u > +#define NCBI_RANDOM_VALUE_82776595395u > +#define NCBI_RANDOM_VALUE_9270550684u These values are generated here: ncbi-blast-2.11.0+-src/c++/scripts/common/impl/define_random_macros.sh I don’t know if we can just define them to fixed values; it should be fine. Debian also has a patch for other problems including the NCBI_SIGNATURE value:
bug#42141: blast+ is not reproducible
reopen 42141 thanks Maxim Cournoyer writes: > Hi, > > Ricardo Wurmus writes: > >> This should be rather easy to fix: >> >> diff -r >> /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include >> /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include-check >> diff -r >> /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h >> /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include-check/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h >> 4,13c4,13 >> < #define NCBI_RANDOM_VALUE_01770246234u >> < #define NCBI_RANDOM_VALUE_12685550394u >> < #define NCBI_RANDOM_VALUE_21952513968u >> < #define NCBI_RANDOM_VALUE_34081691487u >> < #define NCBI_RANDOM_VALUE_41126642990u >> < #define NCBI_RANDOM_VALUE_52363626105u >> < #define NCBI_RANDOM_VALUE_6444644742u >> < #define NCBI_RANDOM_VALUE_72799580837u >> < #define NCBI_RANDOM_VALUE_8216161479u >> < #define NCBI_RANDOM_VALUE_9992434062u >> --- >>> #define NCBI_RANDOM_VALUE_02851596927u >>> #define NCBI_RANDOM_VALUE_14039058594u >>> #define NCBI_RANDOM_VALUE_23204116600u >>> #define NCBI_RANDOM_VALUE_34270143185u >>> #define NCBI_RANDOM_VALUE_41366873742u >>> #define NCBI_RANDOM_VALUE_5703144487u >>> #define NCBI_RANDOM_VALUE_62507785646u >>> #define NCBI_RANDOM_VALUE_73995716134u >>> #define NCBI_RANDOM_VALUE_8907933519u >>> #define NCBI_RANDOM_VALUE_91149060107u > > Not anymore, according to: > > $ guix challenge blast+ > > 1 store items were analyzed: > - 1 (100.0%) were identical > - 0 (0.0%) differed > - 0 (0.0%) were inconclusive This is still a problem: --8<---cut here---start->8--- $ diff -ru /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include-check diff -ru /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include/include/ncbi-tools++/ncbi-tools++/ncbiconf_unix.h /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include-check/include/ncbi-tools++/ncbi-tools++/ncbiconf_unix.h --- /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include/include/ncbi-tools++/ncbi-tools++/ncbiconf_unix.h 1970-01-01 01:00:01.0 +0100 +++ /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include-check/include/ncbi-tools++/ncbi-tools++/ncbiconf_unix.h 1970-01-01 01:00:01.0 +0100 @@ -1095,7 +1095,7 @@ /* Build signature: compiler-name '_' compiler-version '-' configuration '--' platform-name '-' hostname */ -#define NCBI_SIGNATURE "GCC_1030-DebugMTDLL64--x86_64-unknown-linux5.15.10-gnu2.33-localhost" +#define NCBI_SIGNATURE "GCC_1030-DebugMTDLL64--x86_64-unknown-linux5.15.59-gnu2.33-localhost" /* Define to 1 if SQLColAttribute's last argument is an SQLLEN * */ #define NCBI_SQLCOLATTRIBUTE_SQLLEN 1 diff -ru /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include-check/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h --- /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h 1970-01-01 01:00:01.0 +0100 +++ /gnu/store/0kbsdr61qpj0vkc6s8g2kbp4dq936n0p-blast+-2.11.0-include-check/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h 1970-01-01 01:00:01.0 +0100 @@ -1,13 +1,13 @@ #define NCBI_RANDOM_VALUE_TYPE Uint4 #define NCBI_RANDOM_VALUE_MIN 0 #define NCBI_RANDOM_VALUE_MAX 0xu -#define NCBI_RANDOM_VALUE_03249030781u -#define NCBI_RANDOM_VALUE_13573796697u -#define NCBI_RANDOM_VALUE_22130009325u -#define NCBI_RANDOM_VALUE_34284761029u -#define NCBI_RANDOM_VALUE_43467737853u -#define NCBI_RANDOM_VALUE_53267844710u -#define NCBI_RANDOM_VALUE_64107058373u -#define NCBI_RANDOM_VALUE_7166436459u -#define NCBI_RANDOM_VALUE_8960927418u -#define NCBI_RANDOM_VALUE_93839848519u +#define NCBI_RANDOM_VALUE_02845495105u +#define NCBI_RANDOM_VALUE_12158634051u +#define NCBI_RANDOM_VALUE_24072202242u +#define NCBI_RANDOM_VALUE_3902228395u +#define NCBI_RANDOM_VALUE_41353323915u +#define NCBI_RANDOM_VALUE_5574823513u +#define NCBI_RANDOM_VALUE_64119501261u +#define NCBI_RANDOM_VALUE_72477640938u +#define NCBI_RANDOM_VALUE_82776595395u +#define NCBI_RANDOM_VALUE_9270550684u --8<---cut here---end--->8--- -- Ricardo
bug#42141: blast+ is not reproducible
Hi, Ricardo Wurmus writes: > This should be rather easy to fix: > > diff -r /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include > /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include-check > diff -r > /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h > > /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include-check/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h > 4,13c4,13 > < #define NCBI_RANDOM_VALUE_01770246234u > < #define NCBI_RANDOM_VALUE_12685550394u > < #define NCBI_RANDOM_VALUE_21952513968u > < #define NCBI_RANDOM_VALUE_34081691487u > < #define NCBI_RANDOM_VALUE_41126642990u > < #define NCBI_RANDOM_VALUE_52363626105u > < #define NCBI_RANDOM_VALUE_6444644742u > < #define NCBI_RANDOM_VALUE_72799580837u > < #define NCBI_RANDOM_VALUE_8216161479u > < #define NCBI_RANDOM_VALUE_9992434062u > --- >> #define NCBI_RANDOM_VALUE_02851596927u >> #define NCBI_RANDOM_VALUE_14039058594u >> #define NCBI_RANDOM_VALUE_23204116600u >> #define NCBI_RANDOM_VALUE_34270143185u >> #define NCBI_RANDOM_VALUE_41366873742u >> #define NCBI_RANDOM_VALUE_5703144487u >> #define NCBI_RANDOM_VALUE_62507785646u >> #define NCBI_RANDOM_VALUE_73995716134u >> #define NCBI_RANDOM_VALUE_8907933519u >> #define NCBI_RANDOM_VALUE_91149060107u Not anymore, according to: --8<---cut here---start->8--- $ guix challenge blast+ 1 store items were analyzed: - 1 (100.0%) were identical - 0 (0.0%) differed - 0 (0.0%) were inconclusive --8<---cut here---end--->8--- That's for blast+ 2.11.0. Closing! Maxim
bug#42141: blast+ is not reproducible
This should be rather easy to fix: --8<---cut here---start->8--- diff -r /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include-check diff -r /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h /gnu/store/3y97kfanv9ynxnahyykixchlbpbyvjmm-blast+-2.10.1-include-check/include/ncbi-tools++/ncbi-tools++/ncbi_random_macro.h 4,13c4,13 < #define NCBI_RANDOM_VALUE_01770246234u < #define NCBI_RANDOM_VALUE_12685550394u < #define NCBI_RANDOM_VALUE_21952513968u < #define NCBI_RANDOM_VALUE_34081691487u < #define NCBI_RANDOM_VALUE_41126642990u < #define NCBI_RANDOM_VALUE_52363626105u < #define NCBI_RANDOM_VALUE_6444644742u < #define NCBI_RANDOM_VALUE_72799580837u < #define NCBI_RANDOM_VALUE_8216161479u < #define NCBI_RANDOM_VALUE_9992434062u --- > #define NCBI_RANDOM_VALUE_02851596927u > #define NCBI_RANDOM_VALUE_14039058594u > #define NCBI_RANDOM_VALUE_23204116600u > #define NCBI_RANDOM_VALUE_34270143185u > #define NCBI_RANDOM_VALUE_41366873742u > #define NCBI_RANDOM_VALUE_5703144487u > #define NCBI_RANDOM_VALUE_62507785646u > #define NCBI_RANDOM_VALUE_73995716134u > #define NCBI_RANDOM_VALUE_8907933519u > #define NCBI_RANDOM_VALUE_91149060107u --8<---cut here---end--->8--- -- Ricardo
