Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:37 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the ArrayExpressHTS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/ArrayExpressHTS.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 79/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ArrayExpressHTS 1.44.0 (landing page) Angela Goncalves
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | ... NOT SUPPORTED ... | ||||||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ArrayExpressHTS |
Version: 1.44.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ArrayExpressHTS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ArrayExpressHTS_1.44.0.tar.gz |
StartedAt: 2022-04-12 10:22:03 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 10:28:07 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 363.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ArrayExpressHTS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ArrayExpressHTS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ArrayExpressHTS_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ArrayExpressHTS.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ArrayExpressHTS/DESCRIPTION’ ... OK * this is package ‘ArrayExpressHTS’ version ‘1.44.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘ArrayExpressHTS’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘Rsamtools’ A package should be listed in only one of these fields. Versioned 'LinkingTo' value for ‘Rhtslib’ is only usable in R >= 3.0.2 * checking top-level files ... OK * checking for left-over 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 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 ... NOTE Packages in Depends field not imported from: ‘sampling’ ‘snow’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘assignPipelineOptions’ ‘createServerLog’ ‘getPipelineOption’ ‘processOneProjectAlignment’ ‘processOneProjectAlnReport’ ‘processOneProjectEstimation’ ‘processOneProjectRawReport’ ‘setProjectData’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Tue Apr 12 10:25:25 2022 [AEHTS] Setting Options Step 1 Tue Apr 12 10:25:25 2022 [AEHTS] Setting Options Step 2 Tue Apr 12 10:25:25 2022 [AEHTS] Setting Options Step 3 Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING *** Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] fasta_formatter not found Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location. Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING *** Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] cufflinks not found Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location. Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING *** Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] samtools not found Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location. Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING *** Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] bwa not found Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location. Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING *** Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] mmseq not found Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location. Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING *** Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] bam2hits not found Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location. Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING *** Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] bowtie not found Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location. Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] *** WARNING *** Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] tophat not found Tue Apr 12 10:25:25 2022 [AEHTS] Tue Apr 12 10:25:25 2022 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location. Tue Apr 12 10:25:25 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 10:25:25 2022 [AEHTS] calculate_dustyScore: no visible global function definition for ‘srswor’ cleanupCluster: no visible global function definition for ‘stopCluster’ cleanupCluster: no visible global function definition for ‘cleanupClusters’ createServerLog: no visible global function definition for ‘sinkWorkerOutput’ cufflinks_to_granges: no visible global function definition for ‘Rle’ fastq_to_shortreadq: no visible global function definition for ‘subseq’ getEnsemblAnnotation: no visible global function definition for ‘.path.package’ make_indexes_old: no visible global function definition for ‘subseq’ plot_readoccurence_cdf: no visible global function definition for ‘srswor’ prepareCluster: no visible global function definition for ‘makeCluster’ prepareCluster: no visible global function definition for ‘mergeClusters’ prepareCluster: no visible global function definition for ‘clusterApply’ prepareCluster: no visible global function definition for ‘clusterEvalQ’ readSDRF: no visible global function definition for ‘read.AnnotatedDataFrame’ runProjects: no visible global function definition for ‘clusterApply’ runProjects: no visible global function definition for ‘clusterEvalQ’ runProjects: no visible global function definition for ‘clusterApplyLB’ Undefined global functions or variables: .path.package Rle cleanupClusters clusterApply clusterApplyLB clusterEvalQ makeCluster mergeClusters read.AnnotatedDataFrame sinkWorkerOutput srswor stopCluster subseq * 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 C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * 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 is not available File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/ArrayExpressHTS/libs/ArrayExpressHTS.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (C) Found ‘_printf’, possibly from ‘printf’ (C) Found ‘_putchar’, possibly from ‘putchar’ (C) Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C) Found ‘_srand48’, possibly from ‘srand48’ (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. 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’ for details.
ArrayExpressHTS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ArrayExpressHTS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘ArrayExpressHTS’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c addXS.c -o addXS.o addXS.c:42:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration] Rprintf("What?\n"); ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fltbam.c -o fltbam.o fltbam.c:40:19: warning: passing 'unsigned char [50]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] return(strcmp(k1->str, k2->str) == 0); ^~~~~~~ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/string.h:77:25: note: passing argument to parameter '__s1' here int strcmp(const char *__s1, const char *__s2); ^ fltbam.c:40:28: warning: passing 'unsigned char [50]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] return(strcmp(k1->str, k2->str) == 0); ^~~~~~~ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/string.h:77:43: note: passing argument to parameter '__s2' here int strcmp(const char *__s1, const char *__s2); ^ fltbam.c:45:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration] Rprintf("ID: %s, %d\n", k->str, k->length); ^ fltbam.c:51:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration] Rprintf( "\tIndexes for %d mismatches of length %d: ", v->mm, v->length ); ^ fltbam.c:70:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration] Rprintf( "Welcome, creating structures...\n" ); ^ fltbam.c:91:9: warning: implicit declaration of function 'Rf_error' is invalid in C99 [-Wimplicit-function-declaration] Rf_error("Fail to open BAM file %s\n", argv[1]); ^ fltbam.c:125:24: warning: passing 'unsigned char [50]' to parameter of type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign] strcpy(k->str, bam1_qname(line)); ^~~~~~ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_string.h:83:27: note: expanded from macro 'strcpy' __builtin___strcpy_chk (dest, __VA_ARGS__, __darwin_obsz (dest)) ^~~~ fltbam.c:126:36: warning: passing 'unsigned char [50]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k->length = strlen(k->str); ^~~~~~ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/string.h:82:28: note: passing argument to parameter '__s' here size_t strlen(const char *__s); ^ fltbam.c:215:9: warning: implicit declaration of function 'Rf_error' is invalid in C99 [-Wimplicit-function-declaration] Rf_error("Fail to open BAM file %s\n", argv[1]); ^ fltbam.c:225:9: warning: implicit declaration of function 'Rf_error' is invalid in C99 [-Wimplicit-function-declaration] Rf_error("Fail to open BAM file %s\n", argv[2]); ^ In file included from fltbam.c:4: ./hashtable_itr.h:32:1: warning: inline function 'hashtable_iterator_key' is not defined [-Wundefined-inline] hashtable_iterator_key(struct hashtable_itr *i); ^ fltbam.c:189:18: note: used here kk = hashtable_iterator_key(itr); ^ In file included from fltbam.c:4: ./hashtable_itr.h:46:1: warning: inline function 'hashtable_iterator_value' is not defined [-Wundefined-inline] hashtable_iterator_value(struct hashtable_itr *i); ^ fltbam.c:190:17: note: used here v = hashtable_iterator_value(itr); ^ 12 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c functions.c -o functions.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c hashtable.c -o hashtable.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c hashtable_itr.c -o hashtable_itr.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c hashtable_utility.c -o hashtable_utility.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sam.c -o sam.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ArrayExpressHTS.so addXS.o bam_plbuf.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o sam.o /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-ArrayExpressHTS/00new/ArrayExpressHTS/libs ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘Biobase’ for request: ‘read.AnnotatedDataFrame’ when loading ‘ArrayExpressHTS’ No methods found in package ‘IRanges’ for requests: ‘Rle’, ‘subseq’ when loading ‘ArrayExpressHTS’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘Biobase’ for request: ‘read.AnnotatedDataFrame’ when loading ‘ArrayExpressHTS’ No methods found in package ‘IRanges’ for requests: ‘Rle’, ‘subseq’ when loading ‘ArrayExpressHTS’ Tue Apr 12 03:41:40 2022 [AEHTS] Setting Options Step 1 Tue Apr 12 03:41:40 2022 [AEHTS] Setting Options Step 2 Tue Apr 12 03:41:40 2022 [AEHTS] Setting Options Step 3 Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] fasta_formatter not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] cufflinks not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] samtools not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] bwa not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] mmseq not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] bam2hits not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] bowtie not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] tophat not found Tue Apr 12 03:41:40 2022 [AEHTS] Tue Apr 12 03:41:40 2022 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location. Tue Apr 12 03:41:40 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:40 2022 [AEHTS] ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location No methods found in package ‘Biobase’ for request: ‘read.AnnotatedDataFrame’ when loading ‘ArrayExpressHTS’ No methods found in package ‘IRanges’ for requests: ‘Rle’, ‘subseq’ when loading ‘ArrayExpressHTS’ Tue Apr 12 03:41:59 2022 [AEHTS] Setting Options Step 1 Tue Apr 12 03:41:59 2022 [AEHTS] Setting Options Step 2 Tue Apr 12 03:41:59 2022 [AEHTS] Setting Options Step 3 Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] fasta_formatter not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] cufflinks not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] samtools not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] bwa not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] mmseq not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] bam2hits not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] bowtie not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] *** WARNING *** Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] tophat not found Tue Apr 12 03:41:59 2022 [AEHTS] Tue Apr 12 03:41:59 2022 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location. Tue Apr 12 03:41:59 2022 [AEHTS] Use .Rprofile to make options persistent. Tue Apr 12 03:41:59 2022 [AEHTS] ** testing if installed package keeps a record of temporary installation path * DONE (ArrayExpressHTS)
ArrayExpressHTS.Rcheck/ArrayExpressHTS-Ex.timings
name | user | system | elapsed | |
ArrayExpressHTS | 0.002 | 0.001 | 0.003 | |
ArrayExpressHTSFastQ | 0.005 | 0.001 | 0.007 | |
isRCloud | 0.001 | 0.000 | 0.001 | |
package-options | 0.001 | 0.001 | 0.002 | |
prepareAnnotation | 0.002 | 0.000 | 0.002 | |
prepareReference | 0.003 | 0.001 | 0.003 | |
processing-options | 0.002 | 0.002 | 0.003 | |