Mike Jiang
| Snapshot Date: 2024-11-20 13:40 -0500 (Wed, 20 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/openCyto |
| git_branch: devel |
| git_last_commit: d3a4d87 |
| git_last_commit_date: 2024-10-29 09:48:49 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-21 11:33 -0500 (Thu, 21 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4456 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1454/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| openCyto 2.19.0 (landing page) Mike Jiang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the openCyto package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/openCyto.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: openCyto |
| Version: 2.19.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL openCyto |
| StartedAt: 2024-11-20 15:14:34 -0500 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 15:15:01 -0500 (Wed, 20 Nov 2024) |
| EllapsedTime: 27.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL openCyto
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘openCyto’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c Hungarian.cpp -o Hungarian.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c cpp11.cpp -o cpp11.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11.hpp:3,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11/declarations.hpp:13,
from cpp11.cpp:5:
/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11/R.hpp:11: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
|
<command-line>: note: this is the location of the previous definition
/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11/R.hpp:12: warning: "STRICT_R_HEADERS" redefined
12 | #define STRICT_R_HEADERS
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c misc.cpp -o misc.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11.hpp:3,
from misc.cpp:1:
/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11/R.hpp:11: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
|
<command-line>: note: this is the location of the previous definition
/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11/R.hpp:12: warning: "STRICT_R_HEADERS" redefined
12 | #define STRICT_R_HEADERS
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c rlm.cpp -o rlm.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11.hpp:3,
from rlm.cpp:4:
/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11/R.hpp:11: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
|
<command-line>: note: this is the location of the previous definition
/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11/R.hpp:12: warning: "STRICT_R_HEADERS" redefined
12 | #define STRICT_R_HEADERS
|
<command-line>: note: this is the location of the previous definition
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include/boost/accumulators/statistics/median.hpp:11,
from rlm.cpp:8:
/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
rlm.cpp: In function ‘cpp11::list rlm_cpp(cpp11::doubles_matrix<>, cpp11::doubles, int)’:
rlm.cpp:55:10: warning: ‘scale’ may be used uninitialized [-Wmaybe-uninitialized]
55 | double scale;
| ^~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c solve_LSAP.cpp -o solve_LSAP.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11.hpp:3,
from solve_LSAP.cpp:3:
/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11/R.hpp:11: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
|
<command-line>: note: this is the location of the previous definition
/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11/R.hpp:12: warning: "STRICT_R_HEADERS" redefined
12 | #define STRICT_R_HEADERS
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c unlockNamespace.cpp -o unlockNamespace.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11.hpp:3,
from unlockNamespace.cpp:1:
/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11/R.hpp:11: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
|
<command-line>: note: this is the location of the previous definition
/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include/cpp11/R.hpp:12: warning: "STRICT_R_HEADERS" redefined
12 | #define STRICT_R_HEADERS
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o openCyto.so Hungarian.o cpp11.o misc.o rlm.o solve_LSAP.o unlockNamespace.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-openCyto/00new/openCyto/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (openCyto)