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List: bioc-devel
Subject: [Bioc-devel] Problem building package with devtools+Rcpp
From: sergi.picart () upc ! edu
Date: 2017-09-27 12:11:42
Message-ID: 20170927141142.Horde.XfuR_Up36HhCoovznRTyTLf () correu ! upc ! edu
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Dear developers,
Sorry if the e-mail is duplicated, I had an issue sending it.
I have been struggling with problems building my package DIFFUSTATS a
The problem is related to the usage of Rcpp.
In my current machine, I am unable to build the DIFFUSTATS in the
devel bioconductor:
##############
> build()
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save
--no-restore --quiet \
CMD build '/home/sergi/eraseme3/diffuStats' --no-resave-data --no-manual
* checking for file ‘/home/sergi/eraseme3/diffuStats/DESCRIPTION’ ... OK
* preparing ‘diffuStats’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘diffuStats’ ...
** libs
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include"
-I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/inc
lude"
-I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppParallel/include"
-fpic -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOUR
CE=2 -g -c RcppExports.cpp -o RcppExports.o
In file included from
/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/armadillo:52:0,
from
/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/RcppArmadilloForward.h:46, \
from
/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/RcppArmadillo.h:31, \
from RcppExports.cpp:4:
/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: \
note: #pragma message: WARNING: use of OpenMP disabled; this compiler
doesn't support OpenMP 3.0+
#pragma message ("WARNING: use of OpenMP disabled; this compiler
doesn't support OpenMP 3.0+")
\
^ g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG
-I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include"
-I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/inc
lude"
-I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppParallel/include"
-fpic -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOUR
CE=2 -g -c diffuse_parallel.cpp -o diffuse_parallel.o
In file included from
/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/armadillo:52:0,
from
/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/RcppArmadilloForward.h:46, \
from
/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/RcppArmadillo.h:31, \
from diffuse_parallel.cpp:1:
/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: \
note: #pragma message: WARNING: use of OpenMP disabled; this compiler
doesn't support OpenMP 3.0+
#pragma message ("WARNING: use of OpenMP disabled; this compiler
doesn't support OpenMP 3.0+")
\
^ gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include"
-I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/inclu
de"
-I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppParallel/include"
-fpic -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE
=2 -g -c init.c -o init.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions
-Wl,-z,relro -o diffuStats.so RcppExports.o diffuse_parallel.o init.o
-L/usr/lib/R/lib -lR
installing to /tmp/RtmpRLy9NN/Rinst4d19c0dca4b/diffuStats/libs
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘diffuStats’ in
dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object
'/tmp/RtmpRLy9NN/Rinst4d19c0dca4b/diffuStats/libs/diffuStats.so':
/tmp/RtmpRLy9NN/Rinst4d19c0dca4b/diffuStats/libs/diffuStats.so:
undefined symbol: diffuStats_convertSparse
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/tmp/RtmpRLy9NN/Rinst4d19c0dca4b/diffuStats’
-----------------------------------
ERROR: package installation failed
Error: Command failed (1)
However, this is successful when build(vignettes=FALSE)
##############
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS
Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1
[3] RcppArmadillo_0.7.960.1.2 withr_2.0.0
[5] Rcpp_0.12.12 memoise_1.1.0
[7] digest_0.6.12 RcppParallel_4.3.20
[9] devtools_1.13.3
##############
The local installation of Rcpp, RcppParallel, RcppArmadillo or
devtools seems to have something to do with it, because a machine with
the following configuration (which I cannot use for developing in a
regular basis) works just fine:
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/lapack/liblapack.so.3.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=es_ES.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_1.13.2
loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1
[3] RcppArmadillo_0.7.900.2.0 withr_1.0.2
[5] Rcpp_0.12.11 memoise_1.1.0
[7] digest_0.6.12 RcppParallel_4.3.20
##############
If I try other actions, such as devtools::document or load_all:
Error in dyn.load(dllfile) :
unable to load shared object
'/home/sergi/all/devel/rpackages/diffuStats/src/diffuStats.so':
/home/sergi/all/devel/rpackages/diffuStats/src/diffuStats.so:
undefined symbol: diffuStats_convertSparse
Where convertSparse is the first function in the exported c++ functions
##############
I have tried addressing the OpenMP 3.0 warning without success.
However, I think the problem lies in the compilation.
I have updated the R version, also re-run
Rcpp::compileAttributes()
And the problem persists whatever I do. I might be missing something
obvious...
Any help will be appreciated,
Sergio
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