bug#22153: Make check fails
Hello, And sorry for replying so late. A few days ago, I repeated the build under /tmp and all unit tests passed. Could've been related to the issue above. I'd have to repeat the guix build above in the same directory once I'm logged on to the HPC's node to get you the requested results. Regards, Dennis. On 13 December 2015 at 14:09, Ludovic Courtès wrote: > Hi, > > Dennis Mungai skribis: > > > + > GUIX_DAEMON_SOCKET=/home/administrator/source.build/GCC.buildenv/guix-0.9.0/t-register-39139/var/guix/guix/daemon-socket/socket > > + export NIX_IGNORE_SYMLINK_STORE NIX_STORE_DIR NIX_STATE_DIR > NIX_LOG_DIR NIX_DB_DIR GUIX_DAEMON_SOCKET > > ++ echo > /home/administrator/source.build/GCC.buildenv/guix-0.9.0/t-register-39139/var/guix/guix/daemon-socket/socket > > ++ wc -c > > + '[' 109 -ge 108 ']' > > + exit 77 > > The build directory name is very long, which means that we are a likely > to hit the kernel’s limitation on the length of socket file names, as in > the snippet above. > > What does this command: > > grep ac_cv_guix_test_socket_file_name_length config.log > > return? > > At configure time, one normally gets a warning: > > socket file name limit may be exceeded when running tests > > (This is not an error because there’s no problem if you don’t run ‘make > check’.) > > In your case I think you would have to build from a shorter directory. > > HTH, > Ludo’. >
bug#22948: Porting ocl-icd to guix fails because of ruby
Hello there, I am porting ocl-icd to guix, see the package here: https://github.com/Brainiarc7/guix-bioinformatics/blob/master/gn/packages/ocl-icd.scm I'm getting bugged by this error everytime I call the build as such from a dev setup: env TEMPDIR=/gnu/tmp GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix build -K ocl-icd Error encountered: guix build: error: build failed: error parsing derivation `/gnu/store/7f9hwk8v9vzghc93m93y94iibvcc3mvd-ruby-2.3.0.tar.xz.drv': expected string `Derive([' The same also happens when I attempt to install any ruby related utilities: guix package -p ~/opt/guix-build-system -i ruby-yard warning: failed to install locale: Invalid argument guix package: error: build failed: error parsing derivation `/gnu/store/7f9hwk8v9vzghc93m93y94iibvcc3mvd-ruby-2.3.0.tar.xz.drv': expected string `Derive([' A bug, perhaps? Regards, Dennis.
bug#22948: Porting ocl-icd to guix fails because of ruby
Hello, And a small update: After running the garbage collector, the problem went away (And saved me about 20GBs under /gnu/store). I'm suspecting this was a corrupt store. On 9 March 2016 at 16:33, Ludovic Courtès wrote: > Dennis Mungai skribis: > > > env TEMPDIR=/gnu/tmp GUIX_PACKAGE_PATH=../guix-bioinformatics > > ./pre-inst-env guix build -K ocl-icd > > Note that setting TEMPDIR here (or even TMPDIR) has no effect, since > it’s the ‘guix-daemon’ process, not ‘guix build’, that creates temporary > files. > > > Error encountered: > > > > guix build: error: build failed: error parsing derivation > > `/gnu/store/7f9hwk8v9vzghc93m93y94iibvcc3mvd-ruby-2.3.0.tar.xz.drv': > > expected string `Derive([' > > Could you send the content of the file above? > > It looks like your store may be be corrupt. Did you modify files by > hand under /gnu/store? This would void your warranty. :-) > > Thanks, > Ludo’. >
bug#23055: wget within guix fails to resolve FQDNs when used as an input (native or otherwise)
Hello David, Thanks for the clarification. Seems Arrayfire will need several modify-phases statements to clean up the current build system and in addition, port Boost.Compute to GNU Guix as an input. Will do, and provide feedback on the same. Thanks and regards, Dennis Mungai. On 18 March 2016 at 21:15, Thompson, David wrote: > On Fri, Mar 18, 2016 at 2:04 PM, Dennis Mungai wrote: > > > As you can see in the first part, fetching BoostCompute fails because the > > specified MD5 hash fails, and as a result, the build system falls back to > > fetching the same with wget (see second snippet). > > > > The second part fails because wget fails to resolve the FQDN entry > > github.com. > > > > However, when invoking wget directly, both the local instalation and the > > Guix installation, the FQDN can be resolved correctly and the associated > > file fetched successfully: > > > > /gnu/store/w50mfvfzyjzpcbyw3lll7hm4j457jhb0-wget-1.17.1/bin/wget > > https://github.com/boostorg/compute/archive/v0.5.tar.gz > > > > Would this qualify as a bug filed against wget in Guix, or does the > problem > > lie elsewhere? > > In Guix, builds are performed in an isolated container where there is > *no* external network access. It must be this way because otherwise > builds would be non-deterministic. The only exception is for "fixed > output derivations", whose checksum is known in advance, which > wouldn't be the case here. So, the problem lies with Arrayfire's > build system. A build system really shouldn't download from the net. > It should use what the system has provided for it. In my experience, > build systems that try to download from the net usually try to find > something to use locally first. Without knowing anything beyond the > log you've shown me, I would guess that you need to package > BoostCompute first and provide that as an input to Arrayfire. > Hopefully then it won't try to download it. > > Hope this helps! > > - Dave >
bug#23055: wget within guix fails to resolve FQDNs when used as an input (native or otherwise)
Update: All worked out. I was able to port over the dependencies to guix and fed them as inputs to the package in question. All builds as expected. Thanks and regards, Dennis Mungai. On 18 March 2016 at 21:23, Dennis Mungai wrote: > Hello David, > > Thanks for the clarification. > > Seems Arrayfire will need several modify-phases statements to clean up the > current build system and in addition, port Boost.Compute to GNU Guix as an > input. > > Will do, and provide feedback on the same. > > Thanks and regards, > > Dennis Mungai. > > On 18 March 2016 at 21:15, Thompson, David > wrote: > >> On Fri, Mar 18, 2016 at 2:04 PM, Dennis Mungai wrote: >> >> > As you can see in the first part, fetching BoostCompute fails because >> the >> > specified MD5 hash fails, and as a result, the build system falls back >> to >> > fetching the same with wget (see second snippet). >> > >> > The second part fails because wget fails to resolve the FQDN entry >> > github.com. >> > >> > However, when invoking wget directly, both the local instalation and the >> > Guix installation, the FQDN can be resolved correctly and the associated >> > file fetched successfully: >> > >> > /gnu/store/w50mfvfzyjzpcbyw3lll7hm4j457jhb0-wget-1.17.1/bin/wget >> > https://github.com/boostorg/compute/archive/v0.5.tar.gz >> > >> > Would this qualify as a bug filed against wget in Guix, or does the >> problem >> > lie elsewhere? >> >> In Guix, builds are performed in an isolated container where there is >> *no* external network access. It must be this way because otherwise >> builds would be non-deterministic. The only exception is for "fixed >> output derivations", whose checksum is known in advance, which >> wouldn't be the case here. So, the problem lies with Arrayfire's >> build system. A build system really shouldn't download from the net. >> It should use what the system has provided for it. In my experience, >> build systems that try to download from the net usually try to find >> something to use locally first. Without knowing anything beyond the >> log you've shown me, I would guess that you need to package >> BoostCompute first and provide that as an input to Arrayfire. >> Hopefully then it won't try to download it. >> >> Hope this helps! >> >> - Dave >> > >
bug#23055: wget within guix fails to resolve FQDNs when used as an input (native or otherwise)
Hello there, I'm porting Arrayfire to GNU Guix, see https://github.com/Brainiarc7/guix-bioinformatics/blob/master/gn/packages/arrayfire.scm One of the inputs declared is wget, needed as a fall-back when fetching BoostCompute should the Cmake checksums fail. See the build log below: -- Boost version: 1.60.0 -- BoostCompute... -- getting https://github.com/boostorg/compute/archive/v0.5.tar.gz -- validating /tmp/nix-build-arrayfire-3.3.1.drv-0/build/third_party/compute-0.5.tar.gz CMake Warning at CMakeModules/build_boost_compute.cmake:47 (MESSAGE): /tmp/nix-build-arrayfire-3.3.1.drv-0/build/third_party/compute-0.5.tar.gz: Invalid check sum d41d8cd98f00b204e9800998ecf8427e. Expected was 69a52598ac539d3b7f6005a3dd2b6f58 Call Stack (most recent call first): src/backend/opencl/CMakeLists.txt:91 (INCLUDE) -- Trying wget https://github.com/boostorg/compute/archive/v0.5.tar.gz --2016-03-18 17:38:55-- https://github.com/boostorg/compute/archive/v0.5.tar.gz Resolving github.com (github.com)... failed: Name or service not known. wget: unable to resolve host address ‘github.com’ CMake Error at CMakeModules/build_boost_compute.cmake:53 (MESSAGE): /tmp/nix-build-arrayfire-3.3.1.drv-0/build/third_party/compute-0.5.tar.gz: Invalid check sum d41d8cd98f00b204e9800998ecf8427e. Expected was 69a52598ac539d3b7f6005a3dd2b6f58 Call Stack (most recent call first): src/backend/opencl/CMakeLists.txt:91 (INCLUDE) -- Configuring incomplete, errors occurred! See also "/tmp/nix-build-arrayfire-3.3.1.drv-0/build/CMakeFiles/CMakeOutput.log". phase `configure' failed after 2.8 seconds builder for `/gnu/store/4ik93fkxrjy6acihzz5mzjcjkwc5va38-arrayfire-3.3.1.drv' failed with exit code 1 @ build-failed /gnu/store/4ik93fkxrjy6acihzz5mzjcjkwc5va38-arrayfire-3.3.1.drv - 1 builder for `/gnu/store/4ik93fkxrjy6acihzz5mzjcjkwc5va38-arrayfire-3.3.1.drv' failed with exit code 1 guix build: error: build failed: build of `/gnu/store/4ik93fkxrjy6acihzz5mzjcjkwc5va38-arrayfire-3.3.1.drv' failed As you can see in the first part, fetching BoostCompute fails because the specified MD5 hash fails, and as a result, the build system falls back to fetching the same with wget (see second snippet). The second part fails because wget fails to resolve the FQDN entry github.com. However, when invoking wget directly, both the local instalation and the Guix installation, the FQDN can be resolved correctly and the associated file fetched successfully: /gnu/store/w50mfvfzyjzpcbyw3lll7hm4j457jhb0-wget-1.17.1/bin/wget https://github.com/boostorg/compute/archive/v0.5.tar.gz Would this qualify as a bug filed against wget in Guix, or does the problem lie elsewhere? Regards, Dennis.
bug#23504: git 2.7.4 fails to clone repositories over HTTPS sources
Hello there, I'm using git 2.7.4 from a guix profile, and here is my current environment: guix package -p ~/opt/guix-build-system --search-paths warning: failed to install locale: Invalid argument export PATH="/home/lin/opt/guix-build-system/bin:/home/lin/opt/guix-build-system/sbin" export XDG_DATA_DIRS="/home/lin/opt/guix-build-system/share" export GUIX_GTK3_PATH="/home/lin/opt/guix-build-system/lib/gtk-3.0" export INFOPATH="/home/lin/opt/guix-build-system/share/info" export PKG_CONFIG_PATH="/home/lin/opt/guix-build-system/lib/pkgconfig" export GUILE_LOAD_COMPILED_PATH="/home/lin/opt/guix-build-system/lib/guile/2.0/ccache" export C_INCLUDE_PATH="/home/lin/opt/guix-build-system/include" export CPLUS_INCLUDE_PATH="/home/lin/opt/guix-build-system/include" export LIBRARY_PATH="/home/lin/opt/guix-build-system/lib" export ACLOCAL_PATH="/home/lin/opt/guix-build-system/share/aclocal" which env returns: which env /home/lin/opt/guix-build-system/bin/env Now, with git clone example over HTTPS: git clone --branch gn-latest https://github.com/genenetwork/guix-bioinformatics Cloning into 'guix-bioinformatics'... fatal: unable to access 'https://github.com/genenetwork/guix-bioinformatics/': server certificate verification failed. CAfile: none CRLfile: none The system git does not present such an error. What could be wrong with my setup? Missing certificates? At the moment, I've installed the nss-certs package hoping it would be a workaround as these are Mozilla certs, but to no avail. Thanks and regards, Dennis.
bug#23504: git 2.7.4 fails to clone repositories over HTTPS sources
Hmmm, thanks ;-) Perhaps one could set the installation of nss-certs as: 1. A dependency to git, and 2. To print out the environment variable export GTI_SSL_CAPATH once nss-certs is installed. I have seen packages such as gtk3 on guix trigger similar variables to be set when they are installed and loaded from a specific guix profile, as such: guix package -p ~/some-profile -i -some-gtk3-app And then this would be recommended when calling up guix package -p ~/some-profile --search-paths Taken from the email above as an example: export XDG_DATA_DIRS="/home/lin/opt/guix-build-system/share" export GUIX_GTK3_PATH="/home/lin/opt/guix-build-system/lib/gtk-3.0" So yeah, it can be done ;-) On 10 May 2016 at 16:11, Ricardo Wurmus wrote: > > Dennis Mungai writes: > >> Hello there, >> >> I'm using git 2.7.4 from a guix profile, and here is my current environment: >> >> guix package -p ~/opt/guix-build-system --search-paths >> warning: failed to install locale: Invalid argument >> export >> PATH="/home/lin/opt/guix-build-system/bin:/home/lin/opt/guix-build-system/sbin" >> export XDG_DATA_DIRS="/home/lin/opt/guix-build-system/share" >> export GUIX_GTK3_PATH="/home/lin/opt/guix-build-system/lib/gtk-3.0" >> export INFOPATH="/home/lin/opt/guix-build-system/share/info" >> export PKG_CONFIG_PATH="/home/lin/opt/guix-build-system/lib/pkgconfig" >> export >> GUILE_LOAD_COMPILED_PATH="/home/lin/opt/guix-build-system/lib/guile/2.0/ccache" >> export C_INCLUDE_PATH="/home/lin/opt/guix-build-system/include" >> export CPLUS_INCLUDE_PATH="/home/lin/opt/guix-build-system/include" >> export LIBRARY_PATH="/home/lin/opt/guix-build-system/lib" >> export ACLOCAL_PATH="/home/lin/opt/guix-build-system/share/aclocal" >> >> which env returns: >> >> which env >> /home/lin/opt/guix-build-system/bin/env >> >> Now, with git clone example over HTTPS: >> >> git clone --branch gn-latest >> https://github.com/genenetwork/guix-bioinformatics >> Cloning into 'guix-bioinformatics'... >> fatal: unable to access >> 'https://github.com/genenetwork/guix-bioinformatics/': server >> certificate verification failed. CAfile: none CRLfile: none >> >> The system git does not present such an error. >> >> What could be wrong with my setup? Missing certificates? > > Please try this: > > export GIT_SSL_CAPATH=$HOME/.guix-profile/etc/ssl/certs > > Assuming that nss-certs has been installed into $HOME/.guix-profile this > should be enough to make it work. > > I wonder how we can make it easier to tell the user that this > environment variable must be set. > > ~~ Ricardo
bug#23504: git 2.7.4 fails to clone repositories over HTTPS sources
Sure, will do. On 10 May 2016 at 16:38, Ludovic Courtès wrote: > Dennis Mungai skribis: > >> I'm using git 2.7.4 from a guix profile, and here is my current environment: >> >> guix package -p ~/opt/guix-build-system --search-paths >> warning: failed to install locale: Invalid argument >> export >> PATH="/home/lin/opt/guix-build-system/bin:/home/lin/opt/guix-build-system/sbin" >> export XDG_DATA_DIRS="/home/lin/opt/guix-build-system/share" >> export GUIX_GTK3_PATH="/home/lin/opt/guix-build-system/lib/gtk-3.0" >> export INFOPATH="/home/lin/opt/guix-build-system/share/info" >> export PKG_CONFIG_PATH="/home/lin/opt/guix-build-system/lib/pkgconfig" >> export >> GUILE_LOAD_COMPILED_PATH="/home/lin/opt/guix-build-system/lib/guile/2.0/ccache" >> export C_INCLUDE_PATH="/home/lin/opt/guix-build-system/include" >> export CPLUS_INCLUDE_PATH="/home/lin/opt/guix-build-system/include" >> export LIBRARY_PATH="/home/lin/opt/guix-build-system/lib" >> export ACLOCAL_PATH="/home/lin/opt/guix-build-system/share/aclocal" >> >> which env returns: >> >> which env >> /home/lin/opt/guix-build-system/bin/env >> >> Now, with git clone example over HTTPS: >> >> git clone --branch gn-latest >> https://github.com/genenetwork/guix-bioinformatics >> Cloning into 'guix-bioinformatics'... >> fatal: unable to access >> 'https://github.com/genenetwork/guix-bioinformatics/': server >> certificate verification failed. CAfile: none CRLfile: none >> >> The system git does not present such an error. >> >> What could be wrong with my setup? Missing certificates? >> >> At the moment, I've installed the nss-certs package hoping it would be >> a workaround as these are Mozilla certs, but to no avail. > > I think you also need to set the ‘GIT_SSL_CAINFO’ environment variable. > For instance: > > $ guix package -i nss-certs > $ export SSL_CERT_DIR="$HOME/.guix-profile/etc/ssl/certs" > $ export > SSL_CERT_FILE="$HOME/.guix-profile/etc/ssl/certs/ca-certificates.crt" > $ export GIT_SSL_CAINFO="$SSL_CERT_FILE" > > Can you confirm? > > Thanks, > Ludo’.
bug#23504: git 2.7.4 fails to clone repositories over HTTPS sources
Hey there, Sorry for the late reply. I used Pjotr's Guix hacking notes to fix the problem , solution: https://github.com/pjotrp/guix-notes/blob/master/HACKING.org#git-ca-certificates On 10 May 2016 at 16:46, Dennis Mungai wrote: > Sure, will do. > > On 10 May 2016 at 16:38, Ludovic Courtès wrote: >> Dennis Mungai skribis: >> >>> I'm using git 2.7.4 from a guix profile, and here is my current environment: >>> >>> guix package -p ~/opt/guix-build-system --search-paths >>> warning: failed to install locale: Invalid argument >>> export >>> PATH="/home/lin/opt/guix-build-system/bin:/home/lin/opt/guix-build-system/sbin" >>> export XDG_DATA_DIRS="/home/lin/opt/guix-build-system/share" >>> export GUIX_GTK3_PATH="/home/lin/opt/guix-build-system/lib/gtk-3.0" >>> export INFOPATH="/home/lin/opt/guix-build-system/share/info" >>> export PKG_CONFIG_PATH="/home/lin/opt/guix-build-system/lib/pkgconfig" >>> export >>> GUILE_LOAD_COMPILED_PATH="/home/lin/opt/guix-build-system/lib/guile/2.0/ccache" >>> export C_INCLUDE_PATH="/home/lin/opt/guix-build-system/include" >>> export CPLUS_INCLUDE_PATH="/home/lin/opt/guix-build-system/include" >>> export LIBRARY_PATH="/home/lin/opt/guix-build-system/lib" >>> export ACLOCAL_PATH="/home/lin/opt/guix-build-system/share/aclocal" >>> >>> which env returns: >>> >>> which env >>> /home/lin/opt/guix-build-system/bin/env >>> >>> Now, with git clone example over HTTPS: >>> >>> git clone --branch gn-latest >>> https://github.com/genenetwork/guix-bioinformatics >>> Cloning into 'guix-bioinformatics'... >>> fatal: unable to access >>> 'https://github.com/genenetwork/guix-bioinformatics/': server >>> certificate verification failed. CAfile: none CRLfile: none >>> >>> The system git does not present such an error. >>> >>> What could be wrong with my setup? Missing certificates? >>> >>> At the moment, I've installed the nss-certs package hoping it would be >>> a workaround as these are Mozilla certs, but to no avail. >> >> I think you also need to set the ‘GIT_SSL_CAINFO’ environment variable. >> For instance: >> >> $ guix package -i nss-certs >> $ export SSL_CERT_DIR="$HOME/.guix-profile/etc/ssl/certs" >> $ export >> SSL_CERT_FILE="$HOME/.guix-profile/etc/ssl/certs/ca-certificates.crt" >> $ export GIT_SSL_CAINFO="$SSL_CERT_FILE" >> >> Can you confirm? >> >> Thanks, >> Ludo’.
bug#23504: git 2.7.4 fails to clone repositories over HTTPS sources
Also, your workaround worked (in git, at least). I'm not sure if there are other cases affected by this in the wild. On 11 May 2016 at 11:10, Dennis Mungai wrote: > Hey there, > > Sorry for the late reply. > > I used Pjotr's Guix hacking notes to fix the problem , solution: > > https://github.com/pjotrp/guix-notes/blob/master/HACKING.org#git-ca-certificates > > > > On 10 May 2016 at 16:46, Dennis Mungai wrote: >> Sure, will do. >> >> On 10 May 2016 at 16:38, Ludovic Courtès wrote: >>> Dennis Mungai skribis: >>> >>>> I'm using git 2.7.4 from a guix profile, and here is my current >>>> environment: >>>> >>>> guix package -p ~/opt/guix-build-system --search-paths >>>> warning: failed to install locale: Invalid argument >>>> export >>>> PATH="/home/lin/opt/guix-build-system/bin:/home/lin/opt/guix-build-system/sbin" >>>> export XDG_DATA_DIRS="/home/lin/opt/guix-build-system/share" >>>> export GUIX_GTK3_PATH="/home/lin/opt/guix-build-system/lib/gtk-3.0" >>>> export INFOPATH="/home/lin/opt/guix-build-system/share/info" >>>> export PKG_CONFIG_PATH="/home/lin/opt/guix-build-system/lib/pkgconfig" >>>> export >>>> GUILE_LOAD_COMPILED_PATH="/home/lin/opt/guix-build-system/lib/guile/2.0/ccache" >>>> export C_INCLUDE_PATH="/home/lin/opt/guix-build-system/include" >>>> export CPLUS_INCLUDE_PATH="/home/lin/opt/guix-build-system/include" >>>> export LIBRARY_PATH="/home/lin/opt/guix-build-system/lib" >>>> export ACLOCAL_PATH="/home/lin/opt/guix-build-system/share/aclocal" >>>> >>>> which env returns: >>>> >>>> which env >>>> /home/lin/opt/guix-build-system/bin/env >>>> >>>> Now, with git clone example over HTTPS: >>>> >>>> git clone --branch gn-latest >>>> https://github.com/genenetwork/guix-bioinformatics >>>> Cloning into 'guix-bioinformatics'... >>>> fatal: unable to access >>>> 'https://github.com/genenetwork/guix-bioinformatics/': server >>>> certificate verification failed. CAfile: none CRLfile: none >>>> >>>> The system git does not present such an error. >>>> >>>> What could be wrong with my setup? Missing certificates? >>>> >>>> At the moment, I've installed the nss-certs package hoping it would be >>>> a workaround as these are Mozilla certs, but to no avail. >>> >>> I think you also need to set the ‘GIT_SSL_CAINFO’ environment variable. >>> For instance: >>> >>> $ guix package -i nss-certs >>> $ export SSL_CERT_DIR="$HOME/.guix-profile/etc/ssl/certs" >>> $ export >>> SSL_CERT_FILE="$HOME/.guix-profile/etc/ssl/certs/ca-certificates.crt" >>> $ export GIT_SSL_CAINFO="$SSL_CERT_FILE" >>> >>> Can you confirm? >>> >>> Thanks, >>> Ludo’.
