Closed alex-l-kong closed 2 years ago
gfinak
commented
3 years ago All I can gather is it's something with boost. Can you give the recipe to reproduce this. What's the base image? Is it a bioc image or a base ubuntu image? What steps are performed before this?
alex-l-kong
commented
3 years ago @gfinak I do the following before I install cytolib for a Travis build, then I install cytolib from BiocManager (so the bioc image I would assume):
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran40/'
sudo apt-get update
sudo apt-get -y --allow-unauthenticated install r-base r-base-dev
Rscript -e 'dir.create(path=Sys.getenv("R_LIBS_USER"), showWarnings=FALSE, recursive=TRUE)'
Rscript -e 'install.packages("data.table", lib=Sys.getenv("R_LIBS_USER"), repos="http://cran.us.r-project.org")'
Rscript -e 'install.packages("BiocManager", lib=Sys.getenv("R_LIBS_USER"), repos="http://cran.us.r-project.org")'
Rscript -e 'BiocManager::install("cytolib", lib=Sys.getenv("R_LIBS_USER"))'I'm using Bioconductor 3.12 and R 4.0.3.
gfinak
commented
3 years ago This isn't a BioC image since those have R and BioConductor preinstalled. Can you find out what the base image is?
alex-l-kong
commented
3 years ago @gfinak from my Travis logs it's downloading this one: https://bioconductor.org/packages/3.12/bioc/src/contrib/cytolib_2.2.0.tar.gz.
gfinak
commented
3 years ago I'm asking what is the base image used by the docker container.
Greg Finak
On Fri, Jan 15, 2021, 15:12 alex-l-kong notifications@github.com wrote:
@gfinak https://github.com/gfinak from my Travis logs it's downloading this one: https://bioconductor.org/packages/3.12/bioc/src/contrib/cytolib_2.2.0.tar.gz .
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/RGLab/cytolib/issues/46#issuecomment-761245494, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKSI6IR5UMO77CMFBMWBITS2DDT7ANCNFSM4WEPZTQQ .
alex-l-kong
commented
3 years ago @gfinak oh OK, I think you mean related to the distribution of Ubuntu (xenial) we're using. Here's the information under the docker version heading of build system information:
Client:
Version: 18.06.0-ce
API version: 1.38
Go version: go1.10.3
Git commit: 0ffa825
Built: Wed Jul 18 19:11:02 2018
OS/Arch: linux/amd64
Experimental: false
Server:
Engine:
Version: 18.06.0-ce
API version: 1.38 (minimum version 1.12)
Go version: go1.10.3
Git commit: 0ffa825
Built: Wed Jul 18 19:09:05 2018
OS/Arch: linux/amd64
Experimental: falseLet me know if you need more info and/or if I'm still jumping through the wrong hoop. Sorry for the misunderstandings.
gfinak
commented
3 years ago Okay, looks like the boost headers package (BH) was just updated to boost 1.75, and some of the function signatures have changed. In order to work around this you should install BH 1.72.0-3 as part of your CI script, then install cytolib.
apt install wget
wget https://cran.r-project.org/src/contrib/Archive/BH/BH_1.72.0-3.tar.gz
R CMD INSTALL BH_1.72.0-3.tar.gz
Rscript -e 'BiocManager::install("cytolib", lib=Sys.getenv("R_LIBS_USER"))'
mikejiang
commented
3 years ago fixes are pushed to bioc release and devel
alex-l-kong
commented
3 years ago Thanks @gfinak @mikejiang!
danxfreeman
commented
3 years ago I'm still getting boost errors after installing an older version of BH. This is on an Amazon Linux 2 AMI:
[ec2-user@ip-172-31-26-86 ~]$ sudo R --quiet
> packageVersion("BH")
[1] ‘1.72.0.3’
> BiocManager::install("cytolib")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'cytolib'
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/cytolib_2.2.1.tar.gz'
Content type 'application/x-gzip' length 7921607 bytes (7.6 MB)
==================================================
downloaded 7.6 MB
* installing *source* package ‘cytolib’ ...
** using staged installation
checking for a sed that does not truncate output... /usr/bin/sed
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking for pkg-config... /bin/pkg-config
checking pkg-config knows TileDB... no
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking tiledb/tiledb.h usability... no
checking tiledb/tiledb.h presence... no
checking for tiledb/tiledb.h... no
configure: No tiledb is found, build without tiledb...
configure: Parsing cytolib version info ...
configure: CYTOLIB_VERSION=2.2.1
configure: creating ./config.status
config.status: creating inst/include/cytolib/cytolibConfig.h
config.status: creating src/Makevars
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c CytoFrame.cpp -o CytoFrame.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
from CytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c CytoFrameView.cpp -o CytoFrameView.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/CytoFrameView.hpp:12,
from CytoFrameView.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c CytoVFS.cpp -o CytoVFS.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/cytolib/populationTree.hpp:13,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from GatingHierarchy.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c GatingSet.cpp -o GatingSet.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/cytolib/populationTree.hpp:13,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from ../inst/include/cytolib/GatingSet.hpp:14,
from GatingSet.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/cytolib/compensation.hpp:19:0,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/cytolib/populationTree.hpp:13,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from ../inst/include/cytolib/GatingSet.hpp:14,
from GatingSet.cpp:3:
../inst/include/cytolib/global.hpp: In constructor ‘cytolib::GatingSet::GatingSet(std::__cxx11::string, bool, bool, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, bool, cytolib::CytoCtx)’:
../inst/include/cytolib/global.hpp:29:3: warning: ‘fmt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(fmt)
^~~~~~
GatingSet.cpp:30:14: note: ‘fmt’ was declared here
FileFormat fmt;
^~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c GatingSet.pb.cc -o GatingSet.pb.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c H5CytoFrame.cpp -o H5CytoFrame.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/H5CytoFrame.hpp:12,
from H5CytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c MemCytoFrame.cpp -o MemCytoFrame.o
MemCytoFrame.cpp:551:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from MemCytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c POPINDICES.cpp -o POPINDICES.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from POPINDICES.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c calibrationTable.cpp -o calibrationTable.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c compensation.cpp -o compensation.o
In file included from compensation.cpp:3:0:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c dummy.cpp -o dummy.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c ellipse2points.cpp -o ellipse2points.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c gate.cpp -o gate.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from gate.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c global.cpp -o global.o
global.cpp: In function ‘std::__cxx11::string cytolib::s3_to_http(std::__cxx11::string)’:
global.cpp:46:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 1; i < tokens.size(); i++)
~~^~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c in_polygon.cpp -o in_polygon.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c nodeProperties.cpp -o nodeProperties.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from nodeProperties.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spline.cpp -o spline.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c trans_group.cpp -o trans_group.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c transformation.cpp -o transformation.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
In file included from /usr/lib64/R/library/BH/include/boost/config.hpp:61:0,
from /usr/lib64/R/library/BH/include/boost/filesystem/config.hpp:28,
from boost/libs/filesystem/src/platform_config.hpp:81,
from boost/libs/filesystem/src/codecvt_error_category.cpp:12:
/usr/lib64/R/library/BH/include/boost/system/detail/config.hpp:33:31: error: expected ‘;’ at end of member declaration
#define BOOST_SYSTEM_NOEXCEPT BOOST_NOEXCEPT
^
boost/libs/filesystem/src/codecvt_error_category.cpp:31:32: note: in expansion of macro ‘BOOST_SYSTEM_NOEXCEPT’
const char* name() const BOOST_SYSTEM_NOEXCEPT BOOST_OVERRIDE;
^~~~~~~~~~~~~~~~~~~~~
boost/libs/filesystem/src/codecvt_error_category.cpp:31:54: error: ‘BOOST_OVERRIDE’ does not name a type; did you mean ‘BOOST_VERIFY’?
const char* name() const BOOST_SYSTEM_NOEXCEPT BOOST_OVERRIDE;
^~~~~~~~~~~~~~
BOOST_VERIFY
boost/libs/filesystem/src/codecvt_error_category.cpp:32:36: error: expected ‘;’ at end of member declaration
std::string message(int ev) const BOOST_OVERRIDE;
^~~~~
boost/libs/filesystem/src/codecvt_error_category.cpp:32:42: error: ‘BOOST_OVERRIDE’ does not name a type; did you mean ‘BOOST_VERIFY’?
std::string message(int ev) const BOOST_OVERRIDE;
^~~~~~~~~~~~~~
BOOST_VERIFY
make: *** [boost/libs/filesystem/src/codecvt_error_category.o] Error 1
ERROR: compilation failed for package ‘cytolib’
* removing ‘/root/R/x86_64-koji-linux-gnu-library/4.0/cytolib’
The downloaded source packages are in
‘/tmp/RtmppsPhx3/downloaded_packages’
Old packages: 'BH'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(...) :
installation of package ‘cytolib’ had non-zero exit status
> You should use the latest BH version since we've upgraded it source accordingly in the latest patch
danxfreeman
commented
3 years ago It works, thank you
eudoraleer
commented
2 years ago BH
Hi Mike,
I have problem installation this package as dependency in Rshiny. The same problem with the g++ library. I am using Mac OS X, and it works fine installing locally on my computer. Only during deployment to Rshiny creates the same error as described in the post.
Can you assist me with this, thanks!
Best Regards, eudora
mikejiang
commented
2 years ago Since you are using Mac, it should be able to install binary directly from bioconductor latest release without need to compiling
BiocManager::install("cytolib")
eudoraleer
commented
2 years ago Since you are using Mac, it should be able to install binary directly from bioconductor latest release without need to compiling
BiocManager::install("cytolib")
Dear Mike,
Somehow it seems to work now, I cannot remember what I have done to make it work, but anyway, thank you!!
Best Regards, Lu
Describe the bug
This may be related to a comment someone left in #41. I'm installing
cytolibon Ubuntu 16.04 for Travis testing and I get the following traceback happens when I runRscript -e 'BiocManager::install("cytolib", lib=Sys.getenv("R_LIBS_USER"))'. I get very similar tracebacks when I install a library (ex.FlowSOM) that has a cytolib dependency: