search

Yikun / BBS

The Bioconductor Build System
0 stars 0 forks source link

FLAMES.install #7

Open Yikun opened 1 year ago

Yikun commented 1 year ago 
##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL FLAMES
###
##############################################################################
##############################################################################

* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘FLAMES’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppFunctions.cpp -o RcppFunctions.o
In file included from main-functions/../utility/fastq_utils.h:7,
                 from main-functions/match_cell_barcode.h:13,
                 from RcppFunctions.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:185:19: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function]
  185 |         SCOPE int kseq_read(kseq_t *seq) \
      |                   ^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:185:19: note: in definition of macro ‘__KSEQ_READ’
  185 |         SCOPE int kseq_read(kseq_t *seq) \
      |                   ^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’
  240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:12:1: note: in expansion of macro ‘KSEQ_INIT’
   12 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:20: warning: ‘void kseq_destroy(kseq_t*)’ defined but not used [-Wunused-function]
  171 |         SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
      |                    ^~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:20: note: in definition of macro ‘__KSEQ_BASIC’
  171 |         SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
      |                    ^~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’
  240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:12:1: note: in expansion of macro ‘KSEQ_INIT’
   12 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:23: warning: ‘kseq_t* kseq_init(gzFile)’ defined but not used [-Wunused-function]
  165 |         SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
      |                       ^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:23: note: in definition of macro ‘__KSEQ_BASIC’
  165 |         SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
      |                       ^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’
  240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:12:1: note: in expansion of macro ‘KSEQ_INIT’
   12 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c main-functions/match_cell_barcode.cpp -o main-functions/match_cell_barcode.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c utility/edit_dist.cpp -o utility/edit_dist.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c utility/fastq_utils.cpp -o utility/fastq_utils.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c utility/ssw/ssw_cpp.cpp -o utility/ssw/ssw_cpp.o
In file included from utility/ssw/ssw_cpp.cpp:6:
utility/ssw/ssw.h:19:10: fatal error: sse2neon.h: No such file or directory
   19 | #include "sse2neon.h"
      |          ^~~~~~~~~~~~
compilation terminated.
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: utility/ssw/ssw_cpp.o] Error 1
ERROR: compilation failed for package ‘FLAMES’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/FLAMES’
Yikun commented 1 year ago

See also: https://github.com/OliverVoogd/FLAMES/issues/7#issuecomment-1425113873

Yikun commented 1 year ago

Should be fixed by: https://github.com/OliverVoogd/FLAMES/commit/42363bce5ed122bbd1302d5cd6faad55d73487c8 .

martin-g commented 1 year ago

The CHECK fails due to timeout:

<p><span class="filename">FLAMES.Rcheck/00install.out</span></p>
<div class="kunpeng1 hscrollable">
<pre style="padding: 3px;">##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL FLAMES
###
##############################################################################
##############################################################################

* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘FLAMES’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -c RcppFunctions.cpp -o RcppFunctions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -c main-functions/match_cell_barcode.cpp -o main-functions/match_cell_barcode.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -c utility/edit_dist.cpp -o utility/edit_dist.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -c utility/fastq_utils.cpp -o utility/fastq_utils.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -c utility/ssw/ssw_cpp.cpp -o utility/ssw/ssw_cpp.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -c bam.c -o bam.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -c utility/ssw/ssw.c -o utility/ssw/ssw.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o FLAMES.so RcppExports.o RcppFunctions.o main-functions/match_cell_barcode.o utility/edit_dist.o utility/fastq_utils.o utility/ssw/ssw_cpp.o bam.o utility/ssw/ssw.o /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/Rhtslib/usrlib/libhts.a -lcurl
installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-FLAMES/00new/FLAMES/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 (FLAMES)
</pre>
</div><hr>
<h3>Tests output</h3>
<p><span class="filename">FLAMES.Rcheck/tests/testthat.Rout</span></p>
<div class="kunpeng1 hscrollable">
<pre style="padding: 3px;">
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

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.

&gt; library(testthat)
&gt; library(FLAMES)
&gt; 
&gt; test_check("FLAMES")
Writing configuration parameters to:  /tmp/RtmpmuI4cQ/file2de12020492b80/config_file_3006752.json 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
&gt; 
&gt; proc.time()
   user  system elapsed 
 24.000   0.960  24.944 
</pre>
</div><hr>
<h3>Example timings</h3>
<p><span class="filename">FLAMES.Rcheck/FLAMES-Ex.timings</span></p>
<div class="kunpeng1 hscrollable">

name | user | system | elapsed
-- | -- | -- | --

annotation_to_fasta | 1.940 | 0.012 | 1.955 |  

barcode_info_plots | 0.824 | 0.040 | 0.867 |  

bulk_long_pipeline | 1.182 | 0.117 | 3.501 |  

combine_sce | 1.897 | 0.220 | 2.117 |  

create_config | 0.009 | 0.000 | 0.009 |  

create_sce_from_dir | 0.170 | 0.009 | 0.178 |  

create_se_from_dir | 0.970 | 0.053 | 1.424 |  

find_barcode | 0.184 | 0.016 | 0.200 |  

find_isoform | 0.644 | 0.053 | 0.979 |  

get_GRangesList | 0.939 | 0.033 | 3.266 |  

locate_minimap2_dir | 0.003 | 0.001 | 0.004 |  

minimap2_align | 1.248 | 0.060 | 1.749 |  

minimap2_realign | 1.517 | 0.021 | 1.836 |  

parse_gff_tree | 0.586 | 0.024 | 0.695 |  

quantify | 2.998 | 0.228 | 3.508 |  

sc_DTU_analysis | 0.156 | 0.006 | 0.163 |  

sc_heatmap_expression | 288.864 | 12.039 | 891.955 |  

sc_long_multisample_pipeline | 1.378 | 0.032 | 1.410 |  

sc_long_pipeline | 0.165 | 0.000 | 0.165 |  

sc_mutations | 0.163 | 0.000 | 0.162 |  

</div>