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INSTALL report for CytoML on malbec1

This page was generated on 2021-05-06 12:27:17 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the CytoML package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 418/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoML 2.2.2  (landing page)
Mike Jiang , Jake Wagner
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/CytoML
Branch: RELEASE_3_12
Last Commit: 66a7c54
Last Changed Date: 2021-03-09 19:37:52 -0400 (Tue, 09 Mar 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: CytoML
Version: 2.2.2
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CytoML
StartedAt: 2021-05-05 17:26:20 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 17:27:36 -0400 (Wed, 05 May 2021)
EllapsedTime: 76.2 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CytoML
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘CytoML’ ...
** using staged installation
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++ -std=gnu++11 accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: setting cytolib-ml commandline tool path...
configure: Using the following compilation and linking flags
configure:    PKG_CPPFLAGS=-I/usr/include/libxml2
configure:    PKG_LIBS=-lxml2 
configure:    CYTOLIBML_BIN=/usr/local/bin
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/cytolibml_bin_path.R
** libs
make: R: Command not found
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/flowWorkspace/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12:0,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/CytoML/winFlowJoWorkspace.hpp:439:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/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 /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:0,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function ‘std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)’:
../inst/include/CytoML/flowJoWorkspace.hpp:598:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int j = 0; j < sample_ids.size(); j++)
                  ~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/flowWorkspace/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12:0,
                 from parseFlowJoWorkspace.cpp:9:
../inst/include/CytoML/winFlowJoWorkspace.hpp:439:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/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 /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:0,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function ‘std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)’:
../inst/include/CytoML/flowJoWorkspace.hpp:598:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int j = 0; j < sample_ids.size(); j++)
                  ~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o CytoML.so RcppExports.o parseFlowJoWorkspace.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lxml2 /home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-CytoML/00new/CytoML/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 (CytoML)