Ben Bolstad
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/affyio |
| git_branch: devel |
| git_last_commit: a03ad7f |
| git_last_commit_date: 2024-04-30 10:11:06 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 28/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| affyio 1.75.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
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: 1.75.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:affyio.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings affyio_1.75.0.tar.gz |
| StartedAt: 2024-06-09 23:23:53 -0400 (Sun, 09 Jun 2024) |
| EndedAt: 2024-06-09 23:25:21 -0400 (Sun, 09 Jun 2024) |
| EllapsedTime: 88.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: affyio.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:affyio.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings affyio_1.75.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/affyio.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'affyio/DESCRIPTION' ... OK
* this is package 'affyio' version '1.75.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'affyio' can be installed ... WARNING
Found the following significant warnings:
read_abatch.c:656:176: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:656:182: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:665:146: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:665:152: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:677:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:677:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:689:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:689:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:764:178: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:764:184: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:774:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:774:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:785:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:785:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:795:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:795:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:805:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:805:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:870:178: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:870:184: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:879:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:879:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:890:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:890:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:901:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:901:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:913:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:913:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:924:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:924:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1567:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1567:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1578:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1578:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1589:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1589:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1665:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1665:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1677:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1677:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1689:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1689:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1701:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1701:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1769:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1769:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1780:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1780:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1791:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1791:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1801:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1801:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1811:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:1811:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
read_abatch.c:2661:3: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation]
read_abatch.c:3410:3: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation]
read_bpmap.c:110:18: warning: overflow in conversion from 'long long unsigned int' to 'long int' changes value from '18446744073709551612' to '-4' [-Woverflow]
read_bpmap.c:849:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'SEXP' {aka 'struct SEXPREC *'} [-Wformat=]
read_bpmap.c:698:27: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
read_bpmap.c:655:27: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
read_bpmap.c:603:25: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
read_celfile_generic.c:272:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:294:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:315:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:336:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:357:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:378:3: warning: 'strncpy' output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:399:3: warning: 'strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:420:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:441:3: warning: 'strncpy' output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:464:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:488:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:510:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:532:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:553:3: warning: 'strncpy' output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:575:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:597:3: warning: 'strncpy' output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1270:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1292:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1313:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1334:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1355:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1376:3: warning: 'strncpy' output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1397:3: warning: 'strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1418:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1439:3: warning: 'strncpy' output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1462:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1486:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1508:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1530:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1551:3: warning: 'strncpy' output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1573:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
read_celfile_generic.c:1595:3: warning: 'strncpy' output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation]
read_generic.c:1293:37: warning: format '%f' expects argument of type 'double', but argument 2 has type 'int' [-Wformat=]
See 'F:/biocbuild/bbs-3.20-bioc/meat/affyio.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 ... OK
* 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 ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/affyio/libs/x64/affyio.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs 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: 1 WARNING, 2 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc/meat/affyio.Rcheck/00check.log'
for details.
affyio.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL affyio
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'affyio' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fread_functions.c -o fread_functions.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_abatch.c -o read_abatch.o
read_abatch.c: In function 'read_cel_file_intensities':
read_abatch.c:656:176: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
656 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:656:182: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
656 | 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);
| ~^ ~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:665:146: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
665 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:665:152: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
665 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:677:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
677 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:677:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
677 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:689:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
689 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:689:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
689 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c: In function 'read_cel_file_stddev':
read_abatch.c:764:178: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
764 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:764:184: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
764 | 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);
| ~^ ~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:774:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
774 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:774:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
774 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:785:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
785 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:785:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
785 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:795:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
795 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:795:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
795 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:805:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
805 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:805:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
805 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c: In function 'read_cel_file_npixels':
read_abatch.c:870:178: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
870 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:870:184: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
870 | 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);
| ~^ ~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:879:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
879 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:879:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
879 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:890:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
890 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:890:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
890 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:901:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
901 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:901:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
901 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:913:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
913 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:913:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
913 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:924:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
924 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:924:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
924 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c: In function 'read_gzcel_file_intensities':
read_abatch.c:1567:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1567 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1567:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1567 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1578:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1578 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1578:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1578 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1589:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1589 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1589:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1589 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c: In function 'read_gzcel_file_stddev':
read_abatch.c:1665:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1665 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1665:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1665 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1677:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1677 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1677:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1677 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1689:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1689 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1689:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1689 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1701:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1701 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1701:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1701 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c: In function 'read_gzcel_file_npixels':
read_abatch.c:1769:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1769 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1769:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1769 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1780:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1780 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1780:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1780 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1791:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1791 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1791:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1791 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1801:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1801 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1801:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1801 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1811:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1811 | 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);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c:1811:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1811 | 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);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lld
read_abatch.c: In function 'binary_get_detailed_header_info':
read_abatch.c:2661:3: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation]
2661 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_abatch.c:2661:65: note: length computed here
2661 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_abatch.c: In function 'gzbinary_get_detailed_header_info':
read_abatch.c:3410:3: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation]
3410 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_abatch.c:3410:65: note: length computed here
3410 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function 'ReadBPMAPHeader':
read_bpmap.c:110:18: warning: overflow in conversion from 'long long unsigned int' to 'long int' changes value from '18446744073709551612' to '-4' [-Woverflow]
110 | fseek(infile,-sizeof(float),SEEK_CUR);
| ^~~~~~~~~~~~~~
read_bpmap.c: In function 'ReadBPMAPFileIntoRList':
read_bpmap.c:849:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'SEXP' {aka 'struct SEXPREC *'} [-Wformat=]
849 | error("Unable to open the file %s",filename);
| ~^ ~~~~~~~~
| | |
| | SEXP {aka struct SEXPREC *}
| char *
read_bpmap.c:698:27: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
698 | sprintf(buf, "%d", j+1);
| ^
In function 'readBPMAPSeqIdPositionInfo',
inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3:
read_bpmap.c:698:11: note: 'sprintf' output between 2 and 11 bytes into a destination of size 10
698 | sprintf(buf, "%d", j+1);
| ^~~~~~~~~~~~~~~~~~~~~~~
read_bpmap.c: In function 'ReadBPMAPFileIntoRList':
read_bpmap.c:655:27: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
655 | sprintf(buf, "%d", j+1);
| ^
In function 'readBPMAPSeqIdPositionInfo',
inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3:
read_bpmap.c:655:11: note: 'sprintf' output between 2 and 11 bytes into a destination of size 10
655 | sprintf(buf, "%d", j+1);
| ^~~~~~~~~~~~~~~~~~~~~~~
read_bpmap.c: In function 'ReadBPMAPFileIntoRList':
read_bpmap.c:603:25: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
603 | sprintf(buf, "%d", j+1);
| ^
In function 'readBPMAPSeqIdPositionInfo',
inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3:
read_bpmap.c:603:9: note: 'sprintf' output between 2 and 11 bytes into a destination of size 10
603 | sprintf(buf, "%d", j+1);
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_cdf_xda.c -o read_cdf_xda.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_cdffile2.c -o read_cdffile2.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_celfile_generic.c -o read_celfile_generic.o
read_celfile_generic.c: In function 'generic_get_detailed_header_info':
read_celfile_generic.c:272:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
272 | strncpy(header_info->AlgorithmParameters,"Percentile:",11);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:294:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
294 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:315:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
315 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:336:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
336 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:357:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
357 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:378:3: warning: 'strncpy' output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation]
378 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:399:3: warning: 'strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation]
399 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:420:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
420 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:441:3: warning: 'strncpy' output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation]
441 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:464:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
464 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:488:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
488 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:510:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
510 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:532:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
532 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:553:3: warning: 'strncpy' output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation]
553 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:575:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
575 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:597:3: warning: 'strncpy' output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation]
597 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c: In function 'gzgeneric_get_detailed_header_info':
read_celfile_generic.c:1270:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
1270 | strncpy(header_info->AlgorithmParameters,"Percentile:",11);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1292:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
1292 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1313:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
1313 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1334:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
1334 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1355:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
1355 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1376:3: warning: 'strncpy' output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation]
1376 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1397:3: warning: 'strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation]
1397 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1418:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
1418 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1439:3: warning: 'strncpy' output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation]
1439 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1462:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
1462 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1486:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
1486 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1508:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
1508 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1530:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
1530 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1551:3: warning: 'strncpy' output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation]
1551 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1573:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
1573 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1595:3: warning: 'strncpy' output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation]
1595 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_clf.c -o read_clf.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_generic.c -o read_generic.o
read_generic.c: In function 'print_decode_nvt_triplet':
read_generic.c:1293:37: warning: format '%f' expects argument of type 'double', but argument 2 has type 'int' [-Wformat=]
1293 | Rprintf("Its a float value is %f\n",temp32);
| ~^ ~~~~~~
| | |
| | int
| double
| %d
read_generic.c:1293:5: warning: 'temp32' may be used uninitialized [-Wmaybe-uninitialized]
1293 | Rprintf("Its a float value is %f\n",temp32);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_generic.c:1283:7: note: 'temp32' declared here
1283 | int temp32;
| ^~~~~~
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_pgf.c -o read_pgf.o
read_pgf.c:363:12: warning: 'token_ends_with' defined but not used [-Wunused-function]
363 | static int token_ends_with(char *token, char *ends_in){
| ^~~~~~~~~~~~~~~
gcc -shared -s -static-libgcc -o affyio.dll tmp.def 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 -LF:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-affyio/00new/affyio/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (affyio)