##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings affy_1.89.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/affy.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.89.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Robert D. Shear <rshear@ds.dfci.harvard.edu>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Rafael", "A."),
                      family = "Irizarry",
                      role = "aut",
                      email = "rafa@ds.dfci.harvard.edu"),
               person(given = "Laurent",
                      family = "Gautier",
                      role = "aut",
                      email = "lgautier@gmail.com"),
               person(given = c("Benjamin", "Milo"),
                      family = "Bolstad",
                      role = "aut",
                      email = "bmb@bmbolstad.com"),
               person(given = c("Crispin", "Miller", "with", "contributions", "from", "Magnus", "Astrand"),
                      family = "<Magnus.Astrand@astrazeneca.com>",
                      role = "aut",
                      email = "Magnus.Astrand@astrazeneca.com"),
               person(given = c("Leslie", "M."),
                      family = "Cope",
                      role = "aut",
                      email = "cope@mts.jhu.edu"),
               person(given = "Robert",
                      family = "Gentleman",
                      role = "aut"),
               person(given = "Jeff",
                      family = "Gentry",
                      role = "aut"),
               person(given = "Conrad",
                      family = "Halling",
                      role = "aut",
                      email = "challing@agilixcorp.com"),
               person(given = "Wolfgang",
                      family = "Huber",
                      role = "aut"),
               person(given = "James",
                      family = "MacDonald",
                      role = "aut",
                      email = "jmacdon@u.washington.edu"),
               person(given = c("Benjamin", "I.", "P."),
                      family = "Rubinstein",
                      role = "aut"),
               person(given = "Christopher",
                      family = "Workman",
                      role = "aut",
                      email = "workman@cbs.dtu.dk"),
               person(given = "John",
                      family = "Zhang",
                      role = "aut"),
               person(given = c("Robert", "D."),
                      family = "Shear",
                      role = "cre",
                      email = "rshear@ds.dfci.harvard.edu"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Description field should not start with the package name,
  'This package' or similar.
* 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 ‘affy’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Things done:
      0 (wh:) moved everything related to Cdf-class from 'affy' to 'makecdfenv':
        R/Cdf.R, R/getLocationsData.Cdf.R, locate.name.R, pmormm.R
        R/read.cdffile.R, data/cdf.example.rda, man/Cdf-class.Rd
        man/getLocationsData.Cdf.Rd, man/locate.name.Rd, man/pmormm.Rd
        man/read.cdffile.Rd, src/read_cdffile.c
      o read.affybatch2 reads all cel files together in one big hit
        into an affybatch
      o the baseline in normalize.AffyBatch,invariant can be selected
        using a baseline.type parameter. Also changed "progress" to the 
        more standard "verbose". Seemed to be an error since both PM and
        MM probes were normalized by only PM's where used to establish the 
        normalization, now follows same standard as been introduced for
        normalize.AffyBatch.quantiles.
      o Most normalization routines can now be called with the parameter 
        type which specifies whether to be pmonly, mmonly, both together 
        or both separately. This introduces more consistency to the how
        the normalization routines are actually applied to affybatchs.
      o express() has been completely removed.
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘stats:::C_loess_raw’ ‘stats:::C_lowesp’ ‘stats:::C_lowesw’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls to a base package:
  .C(stats:::C_loess_raw, ...)
  .Fortran(stats:::C_lowesp, ...)
  .Fortran(stats:::C_lowesw, ...)
Packages should not make .C/.Call/.External/.Fortran calls to a base
package. They are not part of the API, for use only by R itself and
subject to change without notice.
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) xy2indices.Rd:51: Escaped LaTeX specials: \_ \_
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'AffyBatch-class.Rd':
  ‘[Biobase:class.eSet]{eSet}’

Non-topic package-anchored link(s) in Rd file 'affy.scalevalue.exprSet.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'expresso.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'generateExprSet-methods.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'justrma.Rd':
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
  ‘[Biobase:class.MIAME]{MIAME}’
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'mas5.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'read.affybatch.Rd':
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
  ‘[Biobase:class.MIAME]{MIAME}’

Non-topic package-anchored link(s) in Rd file 'read.probematrix.Rd':
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
  ‘[Biobase:class.MIAME]{MIAME}’

Non-topic package-anchored link(s) in Rd file 'rma.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AffyBatch-class.Rd: normalize
  normalize-methods.Rd: normalize
  normalize.invariantset.Rd: normalize
  normalize.loess.Rd: normalize
  normalize.quantiles.Rd: normalize
  normalize.quantiles.robust.Rd: normalize
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
mas5                  13.445  0.109  13.562
MAplot                 7.662  0.204   7.887
expresso               5.526  0.028   5.557
ProgressBarText-class  0.947  0.024  16.484
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 6 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/affy.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL affy
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘affy’ ...
** this is package ‘affy’ version ‘1.89.0’
** using staged installation
creating cache ./config.cache
checking how to run the C preprocessor... gcc -std=gnu2x -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include   -g -O2 -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security -c chipbackground.c -o chipbackground.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include   -g -O2 -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security -c getall_locations.c -o getall_locations.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include   -g -O2 -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security -c mas5calls.c -o mas5calls.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include   -g -O2 -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security -c rma2.c -o rma2.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include   -g -O2 -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security -c rma_common.c -o rma_common.o
gcc -std=gnu2x -shared -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/00LOCK-affy/00new/affy/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (affy)