failed to run custom build command for `hdf5-sys v0.5.2`

[slowkow]

Hi!

This looks like a useful tool. I thought I might try it to convert a large .tsv.gz file to .mtx.gz format, but I wasn't able to build it.

Do you know what might be causing the build error here?

I'm using macOS Catalina 10.15.4 (19E287).

$ cargo --version
cargo 1.37.0 (9edd08916 2019-08-02)
$ rustc --version
rustc 1.37.0 (eae3437df 2019-08-13)

Here is the build error:

$ git clone git@github.com:COMBINE-lab/EDS.git
Cloning into 'EDS'...
remote: Enumerating objects: 116, done.
remote: Counting objects: 100% (116/116), done.
remote: Compressing objects: 100% (84/84), done.
remote: Total 366 (delta 57), reused 74 (delta 32), pack-reused 250
Receiving objects: 100% (366/366), 6.53 MiB | 4.16 MiB/s, done.
Resolving deltas: 100% (170/170), done.

$ cd EDS/

$ cd src-rs/

$ cargo build --release
    Updating crates.io index
  Downloaded flate2 v1.0.14
  Downloaded byteorder v1.3.4
  Downloaded rand v0.7.3
  Downloaded libc v0.2.68
  Downloaded miniz_oxide v0.3.6
  Downloaded getrandom v0.1.14
  Downloaded pretty_env_logger v0.3.1
  Downloaded adler32 v1.0.4
  Downloaded libmath v0.2.1
  Downloaded quick-error v1.2.3
  Downloaded regex v1.3.6
  Downloaded hdf5 v0.5.2
  Downloaded aho-corasick v0.7.10
  Downloaded thread_local v1.0.1
  Downloaded memchr v2.3.3
  Downloaded regex-syntax v0.6.17
  Downloaded num-integer v0.1.42
  Downloaded num-traits v0.2.11
  Downloaded termcolor v1.1.0
  Downloaded hdf5-types v0.5.2
  Downloaded hdf5-derive v0.5.2
  Downloaded rand_chacha v0.2.2
  Downloaded chrono v0.4.11
  Downloaded autocfg v1.0.0
  Downloaded ppv-lite86 v0.2.6
  Downloaded ascii v0.9.3
  Downloaded parking_lot v0.8.0
  Downloaded hdf5-sys v0.5.2
  Downloaded error-chain v0.12.2
  Downloaded lock_api v0.2.0
  Downloaded parking_lot_core v0.5.0
  Downloaded ndarray v0.12.1
  Downloaded rand v0.6.5
  Downloaded scopeguard v1.1.0
  Downloaded rand_chacha v0.1.1
  Downloaded rand_jitter v0.1.4
  Downloaded rand_xorshift v0.1.1
  Downloaded rand_isaac v0.1.1
  Downloaded rand_hc v0.1.0
  Downloaded rand_os v0.1.3
  Downloaded smallvec v0.6.13
  Downloaded num-complex v0.2.4
  Downloaded matrixmultiply v0.1.15
  Downloaded maybe-uninit v2.0.0
  Downloaded rand_core v0.3.1
  Downloaded rand_pcg v0.1.2
  Downloaded rand_core v0.4.2
  Downloaded rawpointer v0.1.0
   Compiling memchr v2.3.3
   Compiling cc v1.0.50
   Compiling lazy_static v1.4.0
   Compiling regex-syntax v0.6.17
   Compiling semver-parser v0.7.0
   Compiling libc v0.2.68
   Compiling autocfg v0.1.7
   Compiling maybe-uninit v2.0.0
   Compiling rand_core v0.4.2
   Compiling autocfg v1.0.0
   Compiling proc-macro2 v0.4.30
   Compiling version_check v0.9.1
   Compiling unicode-xid v0.1.0
   Compiling getrandom v0.1.14
   Compiling cfg-if v0.1.10
   Compiling syn v0.15.44
   Compiling log v0.4.8
   Compiling matrixmultiply v0.1.15
   Compiling crc32fast v1.2.0
   Compiling ndarray v0.12.1
   Compiling rawpointer v0.1.0
   Compiling scopeguard v1.1.0
   Compiling bitflags v1.2.1
   Compiling either v1.5.3
   Compiling quick-error v1.2.3
   Compiling termcolor v1.1.0
   Compiling unicode-width v0.1.7
   Compiling byteorder v1.3.4
   Compiling ppv-lite86 v0.2.6
   Compiling ascii v0.9.3
   Compiling adler32 v1.0.4
   Compiling ansi_term v0.11.0
   Compiling vec_map v0.8.1
   Compiling strsim v0.8.0
   Compiling thread_local v1.0.1
   Compiling rand_core v0.3.1
   Compiling lock_api v0.2.0
   Compiling humantime v1.3.0
   Compiling textwrap v0.11.0
   Compiling itertools v0.7.11
   Compiling miniz_oxide v0.3.6
   Compiling rand_xorshift v0.1.1
   Compiling rand_hc v0.1.0
   Compiling rand_isaac v0.1.1
   Compiling rand_chacha v0.1.1
   Compiling rand_pcg v0.1.2
   Compiling rand v0.6.5
   Compiling num-traits v0.2.11
   Compiling num-integer v0.1.42
   Compiling num-complex v0.2.4
   Compiling semver v0.9.0
   Compiling smallvec v0.6.13
   Compiling error-chain v0.12.2
   Compiling aho-corasick v0.7.10
   Compiling rand_os v0.1.3
   Compiling rand_jitter v0.1.4
   Compiling rand v0.4.6
   Compiling time v0.1.42
   Compiling atty v0.2.14
   Compiling hdf5-types v0.5.2
   Compiling clap v2.33.0
   Compiling rustc_version v0.2.3
   Compiling rand_core v0.5.1
   Compiling flate2 v1.0.14
   Compiling rand_chacha v0.2.2
   Compiling parking_lot_core v0.5.0
   Compiling parking_lot v0.8.0
   Compiling rand v0.7.3
   Compiling quote v0.6.13
   Compiling rand v0.3.23
   Compiling libmath v0.2.1
   Compiling chrono v0.4.11
   Compiling libloading v0.5.2
   Compiling regex v1.3.6
   Compiling hdf5-sys v0.5.2
   Compiling env_logger v0.6.2
   Compiling hdf5-derive v0.5.2
   Compiling pretty_env_logger v0.3.1
error: failed to run custom build command for `hdf5-sys v0.5.2`

Caused by:
  process didn't exit successfully: `~/work/github.com/COMBINE-lab/EDS/src-rs/target/release/build/hdf5-sys-500aa5eed06bbeba/build-script-build` (exit code: 101)
--- stdout
Attempting to find HDF5 via Homebrew (any version)...

--- stderr
thread 'main' panicked at 'Unable to locate HDF5 root directory and/or headers.', /Users/kamil/.cargo/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.5.2/build.rs:528:13
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace.

warning: build failed, waiting for other jobs to finish...
error: build failed

It looks like hdf5 is installed.

$ brew install hdf5
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 3 taps (homebrew/core, homebrew/cask and caskroom/versions).
==> New Formulae
wolfmqtt
==> Updated Formulae
glib ✔                            docker-compose-completion         ocrmypdf
go ✔                              doctl                             pgcli
highlight ✔                       erlang                            php-cs-fixer
hugo ✔                            exploitdb                         pkg-config
nss ✔                             fdroidserver                      pueue
angular-cli                       findomain                         pushpin
antibody                          go@1.13                           puzzles
apollo-cli                        helmfile                          pympress
aws-cdk                           homebank                          remind
awsume                            jetty                             rex
balena-cli                        kubebuilder                       root
bartycrouch                       kubernetes-cli                    s3cmd
bedops                            librsvg                           simh
binwalk                           libssh                            skopeo
blis                              libupnp                           spiped
buku                              linkerd                           sslyze
cartridge-cli                     magic-wormhole                    starship
cdk8s                             meilisearch                       stella
cfn-lint                          micro                             step
compcert                          minio                             stress-ng
contentful-cli                    monolith                          terragrunt
convox                            mpd                               tig
csvq                              n                                 tomcat@8
ddgr                              netlify-cli                       uni
devspace                          node@10                           weboob
docfx                             node@12                           wireshark
docker-compose                    nomad
==> Updated Casks
basictex ✔               fanny                    lens                     rectangle
algodoo                  feishu                   loom                     refined-github-safari
altserver                flipper                  macgdbp                  remember-the-milk
appcode-eap              freeyourmusic            macspice                 rescuetime
backblaze                fsnotes                  marvin                   screen
brave-browser-dev        ganache                  mellow                   seamonkey
brightness-sync          gifox                    microsoft-edge-beta      skype-for-business
cabal                    goodsync                 milkman                  slack
cacher                   grids                    multipass                soulver
chromium                 hbuilderx                netron                   terminus
cleanmymac               hstracker                one-switch               termius-beta
cmake                    hubstaff                 openvpn-connect          textual
coconutbattery           jami                     opera-beta               there
corona-tracker           jasp                     pacifist                 tikzit
cozy-drive               jaxx-liberty             pagico                   timely
day-o                    jd-gui                   plex-media-server        tor-browser-alpha
dbvisualizer             joplin                   polymail                 touchdesigner
discord                  keepassxc                porting-kit              tuple
discord-canary           keeweb                   qiyimedia                vscodium
dosbox                   kext-updater             qownnotes                wondershare-filmora
electron-fiddle          kode54-cog               rar                      zeplin
emby-server              latexit                  razorsql
exodus                   lazpaint                 realforce

Warning: hdf5 1.12.0 is already installed and up-to-date
To reinstall 1.12.0, run `brew reinstall hdf5`

[k3yavi]

Hi @slowkow ,

Thanks for raising the issue. In case if you haven't already implemented a workaround this might help link hdf5.
I think hdf5 is usually a pain in the neck and I might make it optional dependency in the future to avoid such issues.

[aldanor]

@slowkow HDF5 1.12 will be supported soon but not yet in hdf5-sys, currently you can either brew install hdf5@1.10 if on mac, or install it from conda.

[aldanor]

There's also an option now (in master, will be released as a version soon) to build HDF5 from source in hdf5 crate, this removes all kinds of dynamic dependencies as it will link it in statically.

[smylab]

How can this problem be solved? I'm having the same problem. Thanks!