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This page was generated on 2024-03-04 11:38:49 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 28/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyio 1.73.0  (landing page)
Ben Bolstad
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/affyio
git_branch: devel
git_last_commit: c7547c4
git_last_commit_date: 2023-10-24 09:31:45 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

BUILD BIN results for affyio on merida1


To the developers/maintainers of the affyio package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/affyio.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: affyio
Version: 1.73.0
Command: rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyio_1.73.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R affyio.buildbin-libdir
StartedAt: 2024-03-02 12:55:17 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 12:55:44 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 27.6 seconds
RetCode: 0
Status:   OK  
PackageFile: affyio_1.73.0.tgz
PackageFileSize: 99.67 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyio_1.73.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R affyio.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=affyio.buildbin-libdir affyio_1.73.0.tar.gz'
>>>>>>> 

* installing *source* package ‘affyio’ ...
** using staged installation
checking for gcc... clang -arch x86_64
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 clang -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch x86_64 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
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 for main in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
checking for pthread_create in -lpthread... yes
checking if we can use pthreads... yes
checking if PTHREAD_STACK_MIN is defined... yes
configure: Enabling threading for affyio
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2   -fPIC  -falign-functions=64 -Wall -g -O2  -c fread_functions.c -o fread_functions.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2   -fPIC  -falign-functions=64 -Wall -g -O2  -c init_package.c -o init_package.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2   -fPIC  -falign-functions=64 -Wall -g -O2  -c read_abatch.c -o read_abatch.o
read_abatch.c:656:207: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i);
                                                                                                                                                                              ~~                              ^~~
                                                                                                                                                                              %lu
read_abatch.c:656:212: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i);
                                                                                                                                                                                    ~~                             ^
                                                                                                                                                                                    %zu
read_abatch.c:665:177: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                ~~                              ^~~
                                                                                                                                                %lu
read_abatch.c:665:182: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                      ~~                             ^~~~
                                                                                                                                                      %zu
read_abatch.c:677:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:677:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:689:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:689:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:764:209: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i);
                                                                                                                                                                                ~~                              ^~~
                                                                                                                                                                                %lu
read_abatch.c:764:214: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i);
                                                                                                                                                                                      ~~                             ^
                                                                                                                                                                                      %zu
read_abatch.c:774:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:774:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:785:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:785:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:795:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:795:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:805:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:805:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:870:209: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i);
                                                                                                                                                                                ~~                              ^~~
                                                                                                                                                                                %lu
read_abatch.c:870:214: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i);
                                                                                                                                                                                      ~~                             ^
                                                                                                                                                                                      %zu
read_abatch.c:879:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:879:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:890:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:890:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:901:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:901:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:913:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:913:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:924:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:924:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:1567:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:1567:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:1578:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:1578:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:1589:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:1589:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:1665:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:1665:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:1677:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:1677:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:1689:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:1689:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:1701:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:1701:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:1769:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:1769:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:1780:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:1780:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:1791:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:1791:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:1801:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:1801:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
read_abatch.c:1811:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                               ~~                              ^~~
                                                                                                                                               %lu
read_abatch.c:1811:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
      Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
                                                                                                                                                     ~~                             ^~~~
                                                                                                                                                     %zu
54 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2   -fPIC  -falign-functions=64 -Wall -g -O2  -c read_bpmap.c -o read_bpmap.o
read_bpmap.c:849:42: warning: format specifies type 'char *' but the argument has type 'SEXP' (aka 'struct SEXPREC *') [-Wformat]
      error("Unable to open the file %s",filename);
                                     ~~  ^~~~~~~~
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2   -fPIC  -falign-functions=64 -Wall -g -O2  -c read_cdf_xda.c -o read_cdf_xda.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2   -fPIC  -falign-functions=64 -Wall -g -O2  -c read_cdffile2.c -o read_cdffile2.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2   -fPIC  -falign-functions=64 -Wall -g -O2  -c read_celfile_generic.c -o read_celfile_generic.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2   -fPIC  -falign-functions=64 -Wall -g -O2  -c read_clf.c -o read_clf.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2   -fPIC  -falign-functions=64 -Wall -g -O2  -c read_generic.c -o read_generic.o
read_generic.c:1293:42: warning: format specifies type 'double' but the argument has type 'int' [-Wformat]
    Rprintf("Its a float  value is %f\n",temp32);
                                   ~~    ^~~~~~
                                   %d
read_generic.c:1293:42: warning: variable 'temp32' is uninitialized when used here [-Wuninitialized]
    Rprintf("Its a float  value is %f\n",temp32);
                                         ^~~~~~
read_generic.c:1283:13: note: initialize the variable 'temp32' to silence this warning
  int temp32;
            ^
             = 0
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2   -fPIC  -falign-functions=64 -Wall -g -O2  -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2   -fPIC  -falign-functions=64 -Wall -g -O2  -c read_pgf.c -o read_pgf.o
read_pgf.c:363:12: warning: unused function 'token_ends_with' [-Wunused-function]
static int token_ends_with(char *token, char *ends_in){
           ^
1 warning generated.
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc/meat/affyio.buildbin-libdir/00LOCK-affyio/00new/affyio/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (affyio)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR affyio.buildbin-libdir/affyio/libs/affyio.so
>>>>>>> 

>>>>>>> Paths before fix:
affyio.buildbin-libdir/affyio/libs/affyio.so:
	affyio.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "affyio.buildbin-libdir/affyio/libs/affyio.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "affyio.buildbin-libdir/affyio/libs/affyio.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "affyio.buildbin-libdir/affyio/libs/affyio.so"

>>>>>>> Paths after fix:
affyio.buildbin-libdir/affyio/libs/affyio.so:
	affyio.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)