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NOTES: (1) a maintainance reboot of lemming prevented these builds to complete on this machine (2) these are the last builds with R 2.6.0 (2007-06-03 r41797) on lamb1 and lemming, next builds will be with R 2.6.0 (2007-06-10 r41908) configured with --enable-strict-barrier |
Package 37/238 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
Biostrings2.5.9H. PagesLast Changed Date: 2007-06-06 03:57:52 -0700 Last Changed Rev: 25216 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | WARNINGS | |
wellington | Linux (SUSE 9.2) | i686 | OK | WARNINGS | ||
churchill | Solaris 2.9 | sparc | OK | WARNINGS | ||
lemming | Windows Server 2003 (32-bit) | x64 | OK | [ WARNINGS ] | skipped |
Package: Biostrings |
Version: 2.5.9 |
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check Biostrings_2.5.9.tar.gz |
RetCode: 0 |
Time: 98.4 seconds |
Status: WARNINGS |
CheckDir: Biostrings.Rcheck |
Warnings: 2 |
* checking for working latex ... OK * using log directory 'D:/biocbld/bbs-2.1-bioc/meat/Biostrings.Rcheck' * using R version 2.6.0 Under development (unstable) (2007-06-03 r41797) * checking for file 'Biostrings/DESCRIPTION' ... OK * this is package 'Biostrings' version '2.5.9' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'Biostrings' can be installed ... WARNING Found the following significant warnings: missing link(s): scoring\_matrices See 'D:/biocbld/bbs-2.1-bioc/meat/Biostrings.Rcheck/00install.out' for details. * checking package directory ... OK * checking for portable file names ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the name space can be loaded with stated dependencies ... OK * checking for unstated 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 ... NOTE testBiostrings: no visible global function definition for 'defineTestSuite' testBiostrings: no visible global function definition for 'runTestSuite' testBiostrings: no visible global function definition for 'printTextProtocol' * checking Rd files ... OK * checking Rd cross-references ... WARNING Missing link(s) in documentation object 'needwunsQS.Rd': scoring\_matrices * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking data for non-ASCII characters ... OK * checking for CRLF line endings in C/C++/Fortran sources/headers ... OK * checking for portable use of $BLAS_LIBS ... OK * creating Biostrings-Ex.R ... OK * checking examples ... OK * checking package vignettes in 'inst/doc' ... OK * creating Biostrings-manual.tex ... OK * checking Biostrings-manual.tex ... OK WARNING: There were 2 warnings, see D:/biocbld/bbs-2.1-bioc/meat/Biostrings.Rcheck/00check.log for details
Biostrings.Rcheck/00install.out:
installing R.css in D:/biocbld/bbs-2.1-bioc/meat/Biostrings.Rcheck ---------- Making package Biostrings ------------ adding build stamp to DESCRIPTION installing NAMESPACE file and metadata making DLL ... making R_init_Biostrings.d from R_init_Biostrings.c making XInteger.d from XInteger.c making XRaw.d from XRaw.c making align_needwunsQS.d from align_needwunsQS.c making char_frequency.d from char_frequency.c making match_boyermoore.d from match_boyermoore.c making match_naive.d from match_naive.c making match_shiftor.d from match_shiftor.c making reverseComplement.d from reverseComplement.c making utils.d from utils.c gcc -Id:/biocbld/bbs-2.1-bioc/R/include -Wall -O3 -std=gnu99 -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -Id:/biocbld/bbs-2.1-bioc/R/include -Wall -O3 -std=gnu99 -c XInteger.c -o XInteger.o gcc -Id:/biocbld/bbs-2.1-bioc/R/include -Wall -O3 -std=gnu99 -c XRaw.c -o XRaw.o gcc -Id:/biocbld/bbs-2.1-bioc/R/include -Wall -O3 -std=gnu99 -c align_needwunsQS.c -o align_needwunsQS.o align_needwunsQS.c: In function `align_needwunsQS': align_needwunsQS.c:25: warning: 'sc' might be used uninitialized in this function align_needwunsQS.c:38: warning: 'lkup_val' might be used uninitialized in this function gcc -Id:/biocbld/bbs-2.1-bioc/R/include -Wall -O3 -std=gnu99 -c char_frequency.c -o char_frequency.o gcc -Id:/biocbld/bbs-2.1-bioc/R/include -Wall -O3 -std=gnu99 -c match_boyermoore.c -o match_boyermoore.o match_boyermoore.c: In function `match_boyermoore': match_boyermoore.c:370: warning: 'i1' might be used uninitialized in this function match_boyermoore.c:370: warning: 'i2' might be used uninitialized in this function match_boyermoore.c:370: warning: 'j1' might be used uninitialized in this function match_boyermoore.c:371: warning: 'c' might be used uninitialized in this function gcc -Id:/biocbld/bbs-2.1-bioc/R/include -Wall -O3 -std=gnu99 -c match_naive.c -o match_naive.o gcc -Id:/biocbld/bbs-2.1-bioc/R/include -Wall -O3 -std=gnu99 -c match_shiftor.c -o match_shiftor.o gcc -Id:/biocbld/bbs-2.1-bioc/R/include -Wall -O3 -std=gnu99 -c reverseComplement.c -o reverseComplement.o gcc -Id:/biocbld/bbs-2.1-bioc/R/include -Wall -O3 -std=gnu99 -c utils.c -o utils.o utils.c: In function `Biostrings_translate_charcpy_from_i1i2': utils.c:240: warning: 'lkup_val' might be used uninitialized in this function utils.c: In function `Biostrings_translate_charcpy_from_subset': utils.c:279: warning: 'lkup_val' might be used uninitialized in this function utils.c: In function `Biostrings_translate_charcpy_to_i1i2': utils.c:319: warning: 'lkup_val' might be used uninitialized in this function utils.c: In function `Biostrings_translate_charcpy_to_subset': utils.c:358: warning: 'lkup_val' might be used uninitialized in this function utils.c: In function `Biostrings_reverse_translate_charcpy_from_i1i2': utils.c:437: warning: 'lkup_val' might be used uninitialized in this function windres -I d:/biocbld/bbs-2.1-bioc/R/include -i Biostrings_res.rc -o Biostrings_res.o gcc -shared -s -o Biostrings.dll Biostrings.def R_init_Biostrings.o XInteger.o XRaw.o align_needwunsQS.o char_frequency.o match_boyermoore.o match_naive.o match_shiftor.o reverseComplement.o utils.o Biostrings_res.o -Ld:/biocbld/bbs-2.1-bioc/R/bin -lR ... DLL made installing DLL installing R files preparing package Biostrings for lazy loading Creating a new generic function for "toString" in "Biostrings" Creating a new generic function for "nchar" in "Biostrings" Creating a new generic function for "as.matrix" in "Biostrings" Creating a new generic function for "as.list" in "Biostrings" Warning in matchSignature(signature, fdef, where) : in the method signature for function "BStringViews" no definition for class: "file" Creating a new generic function for "split" in "Biostrings" Warning in matchSignature(signature, fdef, where) : in the method signature for function "eq" no definition for class: "BioString" installing inst files installing data files installing man source files installing indices not zipping data installing help >>> Building/Updating help pages for package 'Biostrings' Formats: text html latex example chm AAString-class text html latex example chm AMINO_ACID_CODE text html latex example chm BString-class text html latex example chm BStringAlign-class text html latex example chm BStringViews-class text html latex chm BStringViews-constructors text html latex example chm Biostrings-internals text html latex chm DNAString-class text html latex example chm GENETIC_CODE text html latex example chm IUPAC_CODE_MAP text html latex example chm RNAString-class text html latex example chm alphabetFrequency text html latex example chm gregexpr2 text html latex example chm matchPattern text html latex example chm matchProbePair text html latex example chm needwunsQS text html latex example chm missing link(s): scoring\_matrices readFASTA text html latex example chm reverseComplement text html latex example chm scoring_matrices text html latex example chm toComplex text html latex example chm yeastSEQCHR1 text html latex example chm Microsoft HTML Help Compiler 4.74.8702 Compiling d:\biocbld\bbs-2.1-bioc\meat\Biostrings.Rcheck\00_pkg_src\Biostrings\chm\Biostrings.chm Compile time: 0 minutes, 0 seconds 22 Topics 316 Local links 1 Internet link 1 Graphic Created d:\biocbld\bbs-2.1-bioc\meat\Biostrings.Rcheck\00_pkg_src\Biostrings\chm\Biostrings.chm, 44,441 bytes Compression decreased file by 82,089 bytes. adding MD5 sums * DONE (Biostrings)