Open HeinzStuecke opened 2 years ago
It looks like the error is:
CMake Error at cmake_modules/ThirdpartyToolchain.cmake:1349 (message):
Building thrift using ExternalProject requires at least CMake 3.10
but your system only has cmake 3.6.3. We try to check for that, but apparently the check in https://github.com/apache/arrow/blob/master/r/tools/nixlibs.R#L407-L432 isn't detecting that correctly. Could you share what cmake --version
says?
To work around this, you can download and untar the latest cmake release from https://github.com/Kitware/CMake/releases/download/v3.23.2/cmake-3.23.2-linux-x86_64.tar.gz, then export CMAKE=/path/to/bin/cmake
, wherever that ends up when you extract it.
Thank you for your response. cmake --version
returns cmake version 2.8.12.2
.
I also ran wget https://github.com/Kitware/CMake/releases/download/v3.23.2/cmake-3.23.2-linux-x86_64.tar.gz
and then untar cmake-3.23.2-linux-x86_64.tar.gz
but the latter returns bash: untar: command not found ...
.
Update
gunzip
seems to work ... still trying
Okidoki, so I did the following:
wget https://github.com/Kitware/CMake/releases/download/v3.23.2/cmake-3.23.2-linux-x86_64.tar.gz
gunzip cmake-3.23.2-linux-x86_64.tar.gz
export CMAKE=/cmake-3.23.2-linux-x86_64.tar
cmake --version
Which still returns cmake version 2.8.12.2
and I seem to get the same error message when installing arrow
Using username "username".
username@gateway.hpc.university.org's password:
Access denied
username@gateway.hpc.university.org's password:
Access denied
username@gateway.hpc.university.org's password:
Access denied
username@gateway.hpc.university.org's password:
Last login: Thu Jun 23 13:23:12 2022 from see120.see.university.org
+------------------------------------------------------------------------------+
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+------------------------------------------------------------------------------+
/usr/bin/id: cannot find name for group ID 1242206
[username@frontend01 ~]$ cmake --version
cmake version 2.8.12.2
[username@frontend01 ~]$ ^C
[username@frontend01 ~]$ wget
wget: missing URL
Usage: wget [OPTION]... [URL]...
Try `wget --help' for more options.
[username@frontend01 ~]$ wget https://github.com/Kitware/CMake/releases/download/v3.23.2/cmake-3.23.2-linux-x86_64.tar.gz
--2022-06-23 14:44:19-- https://github.com/Kitware/CMake/releases/download/v3.23.2/cmake-3.23.2-linux-x86_64.tar.gz
Resolving github.com (github.com)... 140.82.121.4
Connecting to github.com (github.com)|140.82.121.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/537699/6684c7d5-b152-4b45-8e09-ca27803d17b8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220623%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220623T124420Z&X-Amz-Expires=300&X-Amz-Signature=2e1dbbf293c7e69c53aa4a352d3f8d519311b6e1965409dbc7d60abf5ce0113d&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=537699&response-content-disposition=attachment%3B%20filename%3Dcmake-3.23.2-linux-x86_64.tar.gz&response-content-type=application%2Foctet-stream [following]
--2022-06-23 14:44:20-- https://objects.githubusercontent.com/github-production-release-asset-2e65be/537699/6684c7d5-b152-4b45-8e09-ca27803d17b8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220623%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220623T124420Z&X-Amz-Expires=300&X-Amz-Signature=2e1dbbf293c7e69c53aa4a352d3f8d519311b6e1965409dbc7d60abf5ce0113d&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=537699&response-content-disposition=attachment%3B%20filename%3Dcmake-3.23.2-linux-x86_64.tar.gz&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.109.133, 185.199.110.133, 185.199.108.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 46018921 (44M) [application/octet-stream]
Saving to: ‘cmake-3.23.2-linux-x86_64.tar.gz’
100%[======================================>] 46,018,921 15.5MB/s in 2.8s
2022-06-23 14:44:23 (15.5 MB/s) - ‘cmake-3.23.2-linux-x86_64.tar.gz’ saved [46018921/46018921]
[username@frontend01 ~]$ untar cmake-3.23.2-linux-x86_64.tar.gz bash: untar: command not found...
[username@frontend01 ~]$ gunzip cmake-3.23.2-linux-x86_64.tar.gz
[username@frontend01 ~]$ list
bash: list: command not found...
[username@frontend01 ~]$ -- list
bash: --: command not found...
[username@frontend01 ~]$ l--
bash: l--: command not found...
[username@frontend01 ~]$ --l
bash: --l: command not found...
[username@frontend01 ~]$ getwd
bash: getwd: command not found...
[username@frontend01 ~]$ pwd
/home/users/b/username
[username@frontend01 ~]$ ls
cmake-3.23.2-linux-x86_64.tar my_arrow_pkg.tar.gz R slurm-20999955.out
[username@frontend01 ~]$ dir
cmake-3.23.2-linux-x86_64.tar my_arrow_pkg.tar.gz R slurm-20999955.out
[username@frontend01 ~]$ export CMAKE=/path/to/bin/cmake
[username@frontend01 ~]$ module load R/3.6.1
[username@frontend01 ~]$ R
WARNING: ignoring environment value of R_HOME
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> install.packages(arrow)
Error in install.packages(arrow) : object 'arrow' not found
> install.packages("arrow")
Installing package into ‘/beegfs/home/users/b/username/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors
1: 0-Cloud [https]
2: Australia (Canberra) [https]
3: Australia (Melbourne 1) [https]
4: Australia (Melbourne 2) [https]
5: Australia (Perth) [https]
6: Austria [https]
7: Belgium (Brussels) [https]
8: Brazil (PR) [https]
9: Brazil (RJ) [https]
10: Brazil (SP 1) [https]
11: Brazil (SP 2) [https]
12: Bulgaria [https]
13: Canada (MB) [https]
14: Canada (ON 3) [https]
15: Chile (Santiago) [https]
16: China (Beijing 2) [https]
17: China (Beijing 3) [https]
18: China (Hefei) [https]
19: China (Hong Kong) [https]
20: China (Guangzhou) [https]
21: China (Lanzhou) [https]
22: China (Nanjing) [https]
23: China (Shanghai 2) [https]
24: China (Shenzhen) [https]
25: Colombia (Cali) [https]
26: Costa Rica [https]
27: Cyprus [https]
28: Czech Republic [https]
29: Denmark [https]
30: East Asia [https]
31: Ecuador (Cuenca) [https]
32: Ecuador (Quito) [https]
33: Estonia [https]
34: France (Lyon 1) [https]
35: France (Lyon 2) [https]
36: France (Marseille) [https]
37: France (Paris 1) [https]
38: Germany (Erlangen) [https]
39: Germany (Leipzig) [https]
40: Germany (Göttingen) [https]
41: Germany (Münster) [https]
42: Germany (Regensburg) [https]
43: Greece [https]
44: Hungary [https]
45: Iceland [https]
46: India [https]
47: Indonesia (Jakarta) [https]
48: Iran (Mashhad) [https]
49: Italy (Milano) [https]
50: Italy (Padua) [https]
51: Japan (Tokyo) [https]
52: Korea (Gyeongsan-si) [https]
53: Korea (Seoul 1) [https]
54: Korea (Ulsan) [https]
55: Malaysia [https]
56: Mexico (Mexico City) [https]
57: Morocco [https]
58: Netherlands [https]
59: New Zealand [https]
60: Norway [https]
61: South Africa (Johannesburg) [https]
62: Spain (A Coruña) [https]
63: Spain (Madrid) [https]
64: Sweden (Borås) [https]
65: Sweden (Umeå) [https]
66: Switzerland [https]
67: Taiwan (Taipei) [https]
68: Turkey (Denizli) [https]
69: Turkey (Istanbul) [https]
70: Turkey (Mersin) [https]
71: UK (Bristol) [https]
72: UK (London 1) [https]
73: USA (IA) [https]
74: USA (KS) [https]
75: USA (MI) [https]
76: USA (OH) [https]
77: USA (OR) [https]
78: USA (TN) [https]
79: USA (TX 1) [https]
80: Uruguay [https]
81: (other mirrors)
Selection: 56
trying URL 'https://cran.itam.mx/src/contrib/arrow_8.0.0.tar.gz'
Content type 'application/x-gzip' length 4796875 bytes (4.6 MB)
==================================================
downloaded 4.6 MB
* installing *source* package ‘arrow’ ...
** package ‘arrow’ successfully unpacked and MD5 sums checked
** using staged installation
*** Found local C++ source: 'tools/cpp'
*** Building libarrow from source
For a faster, more complete installation, set the environment variable NOT_CRAN=true before installing
See install vignette for details:
https://cran.r-project.org/web/packages/arrow/vignettes/install.html
**** arrow
**** Error building Arrow C++. Re-run with ARROW_R_DEV=true for debug information.
------------------------- NOTE ---------------------------
There was an issue preparing the Arrow C++ libraries.
See https://arrow.apache.org/docs/r/articles/install.html
---------------------------------------------------------
ERROR: configuration failed for package ‘arrow’
* removing ‘/beegfs/home/users/b/username/R/x86_64-pc-linux-gnu-library/3.6/arrow’
The downloaded source packages are in
‘/tmp/Rtmpsp8zid/downloaded_packages’
Warning message:
In install.packages("arrow") :
installation of package ‘arrow’ had non-zero exit status
> Using username "username".
[username@frontend01 ~]$ cmake --version
cmake version 2.8.12.2
[username@frontend01 ~]$ ^C
[username@frontend01 ~]$ wget
wget: missing URL
Error: unexpected symbol in "Using username"
> username@gateway.hpc.university.org's password:
+ Access denied
+ username@gateway.hpc.university.org's password:
Error: unexpected string constant in:
"Access denied
username@gateway.hpc.university.org'"
> Access denied
Error: unexpected symbol in "Access denied"
> username@gateway.hpc.university.org's password:
--2022-06-23 14:44:19-- https://github.com+
> quit()
Save workspace image? [y/n/c]: n
[username@frontend01 ~]$ export CMAKE=/my_arrow_pkg.tar.gz
[username@frontend01 ~]$ cmake --version
cmake version 2.8.12.2
[username@frontend01 ~]$ export CMAKE=/my_arrow_pkg.tar.gz
[username@frontend01 ~]$ ^C
[username@frontend01 ~]$ ^C
[username@frontend01 ~]$ dir
cmake-3.23.2-linux-x86_64.tar my_arrow_pkg.tar.gz R slurm-20999955.out
[username@frontend01 ~]$ export CMAKE=/cmake-3.23.2-linux-x86_64.tar
[username@frontend01 ~]$ cmake --version
cmake version 2.8.12.2
[username@frontend01 ~]$ ^C
[username@frontend01 ~]$ ^C
[username@frontend01 ~]$ R
WARNING: ignoring environment value of R_HOME
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> install.packages("arrow")
Installing package into ‘/beegfs/home/users/b/username/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors
1: 0-Cloud [https]
2: Australia (Canberra) [https]
3: Australia (Melbourne 1) [https]
4: Australia (Melbourne 2) [https]
5: Australia (Perth) [https]
6: Austria [https]
7: Belgium (Brussels) [https]
8: Brazil (PR) [https]
9: Brazil (RJ) [https]
10: Brazil (SP 1) [https]
11: Brazil (SP 2) [https]
12: Bulgaria [https]
13: Canada (MB) [https]
14: Canada (ON 3) [https]
15: Chile (Santiago) [https]
16: China (Beijing 2) [https]
17: China (Beijing 3) [https]
18: China (Hefei) [https]
19: China (Hong Kong) [https]
20: China (Guangzhou) [https]
21: China (Lanzhou) [https]
22: China (Nanjing) [https]
23: China (Shanghai 2) [https]
24: China (Shenzhen) [https]
25: Colombia (Cali) [https]
26: Costa Rica [https]
27: Cyprus [https]
28: Czech Republic [https]
29: Denmark [https]
30: East Asia [https]
31: Ecuador (Cuenca) [https]
32: Ecuador (Quito) [https]
33: Estonia [https]
34: France (Lyon 1) [https]
35: France (Lyon 2) [https]
36: France (Marseille) [https]
37: France (Paris 1) [https]
38: Germany (Erlangen) [https]
39: Germany (Leipzig) [https]
40: Germany (Göttingen) [https]
41: Germany (Münster) [https]
42: Germany (Regensburg) [https]
43: Greece [https]
44: Hungary [https]
45: Iceland [https]
46: India [https]
47: Indonesia (Jakarta) [https]
48: Iran (Mashhad) [https]
49: Italy (Milano) [https]
50: Italy (Padua) [https]
51: Japan (Tokyo) [https]
52: Korea (Gyeongsan-si) [https]
53: Korea (Seoul 1) [https]
54: Korea (Ulsan) [https]
55: Malaysia [https]
56: Mexico (Mexico City) [https]
57: Morocco [https]
58: Netherlands [https]
59: New Zealand [https]
60: Norway [https]
61: South Africa (Johannesburg) [https]
62: Spain (A Coruña) [https]
63: Spain (Madrid) [https]
64: Sweden (Borås) [https]
65: Sweden (Umeå) [https]
66: Switzerland [https]
67: Taiwan (Taipei) [https]
68: Turkey (Denizli) [https]
69: Turkey (Istanbul) [https]
70: Turkey (Mersin) [https]
71: UK (Bristol) [https]
72: UK (London 1) [https]
73: USA (IA) [https]
74: USA (KS) [https]
75: USA (MI) [https]
76: USA (OH) [https]
77: USA (OR) [https]
78: USA (TN) [https]
79: USA (TX 1) [https]
80: Uruguay [https]
81: (other mirrors)
Selection: 5
trying URL 'https://cran.curtin.edu.au/src/contrib/arrow_8.0.0.tar.gz'
Content type 'application/x-gzip' length 4796875 bytes (4.6 MB)
==================================================
downloaded 4.6 MB
* installing *source* package ‘arrow’ ...
** package ‘arrow’ successfully unpacked and MD5 sums checked
** using staged installation
*** Found local C++ source: 'tools/cpp'
*** Building libarrow from source
For a faster, more complete installation, set the environment variable NOT_CRAN=true before installing
See install vignette for details:
https://cran.r-project.org/web/packages/arrow/vignettes/install.html
**** arrow
**** Error building Arrow C++. Re-run with ARROW_R_DEV=true for debug information.
------------------------- NOTE ---------------------------
There was an issue preparing the Arrow C++ libraries.
See https://arrow.apache.org/docs/r/articles/install.html
---------------------------------------------------------
ERROR: configuration failed for package ‘arrow’
* removing ‘/beegfs/home/users/b/username/R/x86_64-pc-linux-gnu-library/3.6/arrow’
The downloaded source packages are in
‘/tmp/Rtmpt8stMG/downloaded_packages’
Warning message:
In install.packages("arrow") :
installation of package ‘arrow’ had non-zero exit status
>
Seems like I've not properly extracted cmake-3.23.2-linux-x86_64.tar.gz
above. I now ran $ tar -xvf cmake-3.23.2-linux-x86_64.tar
and then export CMAKE=/cmake-3.23.2-linux-x86_64
. However, cmake --version
still returns cmake version 2.8.12.2
.
Seems like I've not properly extracted
cmake-3.23.2-linux-x86_64.tar.gz
above. I now ran$ tar -xvf cmake-3.23.2-linux-x86_64.tar
and thenexport CMAKE=/cmake-3.23.2-linux-x86_64
.
Assuming you've extracted it in your current working directory, you'll want export CMAKE=$(pwd)/cmake-3.23.2-linux-x86_64/bin/cmake
However,
cmake --version
still returnscmake version 2.8.12.2
.
Right. The CMAKE
env var is for the arrow R package build script; cmake
won't be affected by it.
Also, my mistake before, it looks like you have a cmake3
installed, which is version 3.6.3. Can you show me what R -e 'system("cmake3 --version", intern = TRUE, ignore.stderr = TRUE)'
returns?
Thank you for your effort. R -e 'system("cmake3 --version", intern = TRUE, ignore.stderr = TRUE)'
returns:
[username@frontend01 ~]$ R -e 'system("cmake3 --version", intern = TRUE, ignore. stderr = TRUE)'
WARNING: ignoring environment value of R_HOME
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> system("cmake3 --version", intern = TRUE, ignore.stderr = TRUE)
[1] "cmake3 version 3.6.3"
[2] ""
[3] "CMake suite maintained and supported by Kitware (kitware.com/cmake)."
>
>
@HeinzStuecke where you able to install R Arrow after updating CMake to version 3.10 or higher?
Hello, I am trying to use the
feather
library within an R-script which I am trying to run on the High Computation Cluster of my university. Apparently, I needarrow
to usefeather
. I installed feather viainstall.packages("feather")
. However, the installation ofinstall.packages("arrow")
fails.Can anyone help me out here?