Multiple platform build/check report for BioC 3.8 - CHECK report for RProtoBufLib on tokay1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RProtoBufLib.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RProtoBufLib_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RProtoBufLib/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RProtoBufLib' version '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'RProtoBufLib' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    include   1.3Mb
    lib       4.4Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  BSD_3_clause
* 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 shell scripts ... 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 ... OK
* 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-3.8-bioc/R/library/RProtoBufLib/libs/i386/RProtoBufLib.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'UsingRProtoBufLib.Rmd'
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RProtoBufLib_1.4.0.tar.gz && rm -rf RProtoBufLib.buildbin-libdir && mkdir RProtoBufLib.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RProtoBufLib.buildbin-libdir RProtoBufLib_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RProtoBufLib_1.4.0.zip && rm RProtoBufLib_1.4.0.tar.gz RProtoBufLib_1.4.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1968k  100 1968k    0     0  2930k      0 --:--:-- --:--:-- --:--:-- 2983k

install for i386

* installing *source* package 'RProtoBufLib' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I../inst/include/ -Iwin/include/    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c GatingSet_pb_lib/GatingSet.pb.cc -o GatingSet_pb_lib/GatingSet.pb.o
In file included from GatingSet_pb_lib/GatingSet.pb.cc:12:0:
win/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]':
win/include/google/protobuf/wire_format_lite_inl.h:413:1:   required from here
win/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) {
                       ^
win/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) {
                       ^
win/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]':
win/include/google/protobuf/wire_format_lite_inl.h:414:1:   required from here
win/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) {
                       ^
win/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) {
                       ^
win/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]':
win/include/google/protobuf/wire_format_lite_inl.h:415:1:   required from here
win/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) {
                       ^
win/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) {
                       ^
win/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]':
win/include/google/protobuf/wire_format_lite_inl.h:416:1:   required from here
win/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) {
                       ^
win/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) {
                       ^
win/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]':
win/include/google/protobuf/wire_format_lite_inl.h:417:1:   required from here
win/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) {
                       ^
win/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) {
                       ^
win/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]':
win/include/google/protobuf/wire_format_lite_inl.h:418:1:   required from here
win/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) {
                       ^
win/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) {
                       ^
mkdir -p ""C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/include""
cp -r win/include/google "C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/include"
mkdir -p "C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/lib/i386"
cp  win/lib/i386/libprotobuf.a "C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/lib/i386/libprotobuf.a"
cp GatingSet_pb_lib/GatingSet.pb.o C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/lib/i386/GatingSet.pb.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I../inst/include/ -Iwin/include/    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dummy.cpp -o dummy.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o RProtoBufLib.dll tmp.def dummy.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RProtoBufLib'
    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 'RProtoBufLib' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I../inst/include/ -Iwin/include/    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c GatingSet_pb_lib/GatingSet.pb.cc -o GatingSet_pb_lib/GatingSet.pb.o
In file included from GatingSet_pb_lib/GatingSet.pb.cc:12:0:
win/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]':
win/include/google/protobuf/wire_format_lite_inl.h:413:1:   required from here
win/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) {
                       ^
win/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) {
                       ^
win/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]':
win/include/google/protobuf/wire_format_lite_inl.h:414:1:   required from here
win/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) {
                       ^
win/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) {
                       ^
win/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]':
win/include/google/protobuf/wire_format_lite_inl.h:415:1:   required from here
win/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) {
                       ^
win/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) {
                       ^
win/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]':
win/include/google/protobuf/wire_format_lite_inl.h:416:1:   required from here
win/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) {
                       ^
win/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) {
                       ^
win/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]':
win/include/google/protobuf/wire_format_lite_inl.h:417:1:   required from here
win/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) {
                       ^
win/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) {
                       ^
win/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]':
win/include/google/protobuf/wire_format_lite_inl.h:418:1:   required from here
win/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) {
                       ^
win/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) {
                       ^
mkdir -p ""C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/include""
cp -r win/include/google "C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/include"
mkdir -p "C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/lib/x64"
cp  win/lib/x64/libprotobuf.a "C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/lib/x64/libprotobuf.a"
cp GatingSet_pb_lib/GatingSet.pb.o C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/lib/x64/GatingSet.pb.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I../inst/include/ -Iwin/include/    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dummy.cpp -o dummy.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o RProtoBufLib.dll tmp.def dummy.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RProtoBufLib' as RProtoBufLib_1.4.0.zip
* DONE (RProtoBufLib)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RProtoBufLib' successfully unpacked and MD5 sums checked
In R CMD INSTALL

CHECK report for RProtoBufLib on tokay1

Summary

Command output

Installation output

Tests output

Example timings