Ben Bolstad
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/affyio |
| git_branch: devel |
| git_last_commit: 78cc925 |
| git_last_commit_date: 2024-12-14 19:04:40 -0500 (Sat, 14 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 29/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| affyio 1.77.1 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | OK | ERROR | ERROR | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. |
| Package: affyio |
| Version: 1.77.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:affyio.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings affyio_1.77.1.tar.gz |
| StartedAt: 2024-12-23 18:04:52 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 18:05:01 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 9.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: affyio.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:affyio.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings affyio_1.77.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/affyio.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyio/DESCRIPTION’ ... OK
* this is package ‘affyio’ version ‘1.77.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘affyio’ can be installed ... WARNING
Found the following significant warnings:
read_abatch.c:656:207: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:656:212: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:665:177: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:665:182: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:677:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:677:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:689:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:689:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:764:209: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:764:214: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:774:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:774:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:785:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:785:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:795:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:795:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:805:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:805:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:870:209: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:870:214: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:879:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:879:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:890:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:890:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:901:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:901:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:913:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:913:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:924:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:924:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1567:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1567:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1578:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1578:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1589:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1589:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1665:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1665:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1677:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1677:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1689:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1689:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1701:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1701:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1769:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1769:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1780:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1780:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1791:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1791:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1801:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1801:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1811:176: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_abatch.c:1811:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
read_bpmap.c:849:42: warning: format specifies type 'char *' but the argument has type 'SEXP' (aka 'struct SEXPREC *') [-Wformat]
read_generic.c:1293:42: warning: format specifies type 'double' but the argument has type 'int' [-Wformat]
read_generic.c:1293:42: warning: variable 'temp32' is uninitialized when used here [-Wuninitialized]
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/affyio.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work. If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/affyio/libs/affyio.so’:
Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘_sprintf’, possibly from ‘sprintf’ (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 nor [v]sprintf. 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 examples ... NONE
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/affyio.Rcheck/00check.log’
for details.
affyio.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL affyio
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘affyio’ ...
** using staged installation
checking for gcc... clang -arch arm64
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 arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch arm64 -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 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -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/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c fread_functions.c -o fread_functions.o
clang -arch arm64 -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/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o
clang -arch arm64 -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/arm64/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 '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: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 '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: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 '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:677:181: 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 '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:689:181: 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 '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: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 '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: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 '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:785:181: 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 '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:795:181: 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 '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:805:181: 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 '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: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 '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: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 '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:890:181: 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 '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:901:181: 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 '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:913:181: 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 '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:924:181: 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 '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:1567:181: 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 '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:1578:181: 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 '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:1589:181: 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 '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:1665:181: 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 '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:1677:181: 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 '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:1689:181: 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 '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:1701:181: 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 '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:1769:181: 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 '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:1780:181: 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 '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:1791:181: 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 '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:1801:181: 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 '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:1811:181: 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 arm64 -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/arm64/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 arm64 -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/arm64/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 arm64 -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/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c read_cdffile2.c -o read_cdffile2.o
clang -arch arm64 -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/arm64/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 arm64 -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/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c read_clf.c -o read_clf.o
clang -arch arm64 -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/arm64/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 arm64 -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/arm64/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 arm64 -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/arm64/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 arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/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)