Mike Jiang
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/cytolib |
| Branch: RELEASE_3_6 |
| Last Commit: cc476f0 |
| Last Changed Date: 2017-11-03 18:44:20 -0400 (Fri, 03 Nov 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:30:18 -0400 (Thu, 12 Apr 2018).
| Package 324/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cytolib 1.0.1 Mike Jiang
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: cytolib |
| Version: 1.0.1 |
| Command: rm -rf cytolib.buildbin-libdir cytolib.Rcheck && mkdir cytolib.buildbin-libdir cytolib.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cytolib.buildbin-libdir cytolib_1.0.1.tar.gz >cytolib.Rcheck\00install.out 2>&1 && cp cytolib.Rcheck\00install.out cytolib-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cytolib.buildbin-libdir --install="check:cytolib-install.out" --force-multiarch --no-vignettes --timings cytolib_1.0.1.tar.gz |
| StartedAt: 2018-04-11 23:20:08 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:23:10 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 181.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cytolib.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### rm -rf cytolib.buildbin-libdir cytolib.Rcheck && mkdir cytolib.buildbin-libdir cytolib.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cytolib.buildbin-libdir cytolib_1.0.1.tar.gz >cytolib.Rcheck\00install.out 2>&1 && cp cytolib.Rcheck\00install.out cytolib-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cytolib.buildbin-libdir --install="check:cytolib-install.out" --force-multiarch --no-vignettes --timings cytolib_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cytolib/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cytolib' version '1.0.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'cytolib' can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.0Mb
sub-directories of 1Mb or more:
lib 2.8Mb
libs 4.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.buildbin-libdir/cytolib/libs/i386/cytolib.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck/00check.log'
for details.
cytolib.Rcheck/00install.out
install for i386
* installing *source* package 'cytolib' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c GatingHierarchy.cpp -o GatingHierarchy.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c GatingSet.cpp -o GatingSet.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c GatingSet.pb.cc -o GatingSet.pb.o
In file included from GatingSet.pb.cc:12:0:
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)7u]':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:413:1: required from here
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = long long unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)6u]':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:414:1: required from here
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)15u]':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:415:1: required from here
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = long long int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)16u]':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:416:1: required from here
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = float; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)2u]':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:417:1: required from here
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = double; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)1u]':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:418:1: required from here
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c POPINDICES.cpp -o POPINDICES.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c calibrationTable.cpp -o calibrationTable.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c compensation.cpp -o compensation.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c delimitedMessage.cpp -o delimitedMessage.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c ellipse2points.cpp -o ellipse2points.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c flowData.cpp -o flowData.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c gate.cpp -o gate.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c global.cpp -o global.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c nodeProperties.cpp -o nodeProperties.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c spline.cpp -o spline.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c transformation.cpp -o transformation.o
In file included from transformation.cpp:8:0:
../inst/include/cytolib/transformation.hpp: In constructor 'logTrans::logTrans()':
../inst/include/cytolib/transformation.hpp:230:12: warning: 'logTrans::T' will be initialized after [-Wreorder]
unsigned T; //top value; derived from keyword $PnR for each channel
^
../inst/include/cytolib/transformation.hpp:229:12: warning: 'unsigned int logTrans::scale' [-Wreorder]
unsigned scale;
^
transformation.cpp:273:1: warning: when initialized here [-Wreorder]
logTrans::logTrans():transformation(false,LOG),offset(0),decade(1),T(262144), scale(1){
^
In file included from transformation.cpp:8:0:
../inst/include/cytolib/transformation.hpp: In constructor 'fasinhTrans::fasinhTrans()':
../inst/include/cytolib/transformation.hpp:190:9: warning: 'fasinhTrans::length' will be initialized after [-Wreorder]
double length;//unused at this moment
^
../inst/include/cytolib/transformation.hpp:189:9: warning: 'double fasinhTrans::maxRange' [-Wreorder]
double maxRange;
^
transformation.cpp:281:1: warning: when initialized here [-Wreorder]
fasinhTrans::fasinhTrans():transformation(false,FASINH),length(256),maxRange(262144), T(262144),A(0),M(4.5){
^
mkdir -p "C:/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.buildbin-libdir/cytolib/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.buildbin-libdir/cytolib/lib/i386/libcytolib.a" GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o calibrationTable.o compensation.o delimitedMessage.o ellipse2points.o flowData.o gate.o global.o nodeProperties.o spline.o transformation.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.buildbin-libdir/cytolib/lib/i386/libcytolib.a
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cytolib.dll tmp.def GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o calibrationTable.o compensation.o delimitedMessage.o ellipse2points.o flowData.o gate.o global.o nodeProperties.o spline.o transformation.o C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/lib/i386/libprotobuf.a -lws2_32 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.buildbin-libdir/cytolib/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'cytolib'
finding HTML links ... done
LdFlags html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'cytolib' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c GatingHierarchy.cpp -o GatingHierarchy.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c GatingSet.cpp -o GatingSet.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c GatingSet.pb.cc -o GatingSet.pb.o
In file included from GatingSet.pb.cc:12:0:
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)7u]':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:413:1: required from here
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = long long unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)6u]':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:414:1: required from here
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)15u]':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:415:1: required from here
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = long long int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)16u]':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:416:1: required from here
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = float; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)2u]':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:417:1: required from here
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = double; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)1u]':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:418:1: required from here
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c POPINDICES.cpp -o POPINDICES.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c calibrationTable.cpp -o calibrationTable.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c compensation.cpp -o compensation.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c delimitedMessage.cpp -o delimitedMessage.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c ellipse2points.cpp -o ellipse2points.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c flowData.cpp -o flowData.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c gate.cpp -o gate.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c global.cpp -o global.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c nodeProperties.cpp -o nodeProperties.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c spline.cpp -o spline.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c transformation.cpp -o transformation.o
In file included from transformation.cpp:8:0:
../inst/include/cytolib/transformation.hpp: In constructor 'logTrans::logTrans()':
../inst/include/cytolib/transformation.hpp:230:12: warning: 'logTrans::T' will be initialized after [-Wreorder]
unsigned T; //top value; derived from keyword $PnR for each channel
^
../inst/include/cytolib/transformation.hpp:229:12: warning: 'unsigned int logTrans::scale' [-Wreorder]
unsigned scale;
^
transformation.cpp:273:1: warning: when initialized here [-Wreorder]
logTrans::logTrans():transformation(false,LOG),offset(0),decade(1),T(262144), scale(1){
^
In file included from transformation.cpp:8:0:
../inst/include/cytolib/transformation.hpp: In constructor 'fasinhTrans::fasinhTrans()':
../inst/include/cytolib/transformation.hpp:190:9: warning: 'fasinhTrans::length' will be initialized after [-Wreorder]
double length;//unused at this moment
^
../inst/include/cytolib/transformation.hpp:189:9: warning: 'double fasinhTrans::maxRange' [-Wreorder]
double maxRange;
^
transformation.cpp:281:1: warning: when initialized here [-Wreorder]
fasinhTrans::fasinhTrans():transformation(false,FASINH),length(256),maxRange(262144), T(262144),A(0),M(4.5){
^
mkdir -p "C:/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.buildbin-libdir/cytolib/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.buildbin-libdir/cytolib/lib/x64/libcytolib.a" GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o calibrationTable.o compensation.o delimitedMessage.o ellipse2points.o flowData.o gate.o global.o nodeProperties.o spline.o transformation.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.buildbin-libdir/cytolib/lib/x64/libcytolib.a
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cytolib.dll tmp.def GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o calibrationTable.o compensation.o delimitedMessage.o ellipse2points.o flowData.o gate.o global.o nodeProperties.o spline.o transformation.o C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/lib/x64/libprotobuf.a -lws2_32 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.buildbin-libdir/cytolib/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cytolib' as cytolib_1.0.1.zip
* DONE (cytolib)
In R CMD INSTALL
In R CMD INSTALL
|
cytolib.Rcheck/examples_i386/cytolib-Ex.timings
|
cytolib.Rcheck/examples_x64/cytolib-Ex.timings
|