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cummeRbundバージョンアップしてバグ？

Science R

なにやらcummeRbundが使えなくなった。急に。
cuffdiffのデータ処理をミスったかと思ったが、以前に解析したデータでも同じエラーが出て止まってしまう。

> cuff <- readCufflinks("~/expression/SRSF10/hisat_results/cuffdiff_result")
Creating database ~/expression/SRSF10/hisat_results/cuffdiff_result/cuffData.db
Reading Run Info File ~/expression/SRSF10/hisat_results/cuffdiff_result/run.info
Writing runInfo Table
Reading Read Group Info  ~/expression/SRSF10/hisat_results/cuffdiff_result/read_groups.info
Writing replicates Table
Reading Var Model Info  ~/expression/SRSF10/hisat_results/cuffdiff_result/var_model.info
Writing varModel Table
Reading ~/expression/SRSF10/hisat_results/cuffdiff_result/genes.fpkm_tracking
Checking samples table...
Populating samples table...
 エラー: Column name mismatch.
 追加情報:  50 件以上の警告がありました (最初の 50 個の警告を見るには warnings() を使って下さい) 
> cuff
CuffSet instance with:
	 0 samples
	 0 genes
	 0 isoforms
	 0 TSS
	 0 CDS
	 0 promoters
	 0 splicing
	 0 relCDS

https://support.bioconductor.org/p/97561/#97888
この一週間位の間でみんな困っている模様。

6/19にSQLiteが2.0にバージョンアップしておかしくなった？

Installing package(s) 'cummeRbund'
also installing the dependency 'RSQLite'

 URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/RSQLite_2.0.tgz' を試しています 
Content type 'application/x-gzip' length 3241881 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

これだ。

まずcummeRbundをインストールしておいて、一旦終了。

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> remove.packages("cummeRbund")
Removing package from ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
(as ‘lib’ is unspecified)
> remove.packages("RSQLite")
Removing package from ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
(as ‘lib’ is unspecified)
> biocLite("cummeRbund")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.1 Patched (2017-07-09 r72910).
Installing package(s) ‘cummeRbund’
also installing the dependency ‘RSQLite’

 URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/RSQLite_2.0.tgz' を試しています 
Content type 'application/x-gzip' length 3241881 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

 URL 'https://bioconductor.org/packages/3.5/bioc/bin/macosx/el-capitan/contrib/3.4/cummeRbund_2.18.0.tgz' を試しています 
Content type 'application/x-gzip' length 2825501 bytes (2.7 MB)
==================================================
downloaded 2.7 MB


The downloaded binary packages are in
	/var/folders/sf/3lk5x37135586w0jgqyjq_yc0000gn/T//Rtmp79m1Ga/downloaded_packages

起動し直したらRSQLiteを一旦アンインストールして旧バージョンをインストールし直す。

> remove.packages("RSQLite")
Removing package from ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
(as ‘lib’ is unspecified)
install.packages("devtools")
 URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/devtools_1.13.2.tgz' を試しています 
Content type 'application/x-gzip' length 437492 bytes (427 KB)
==================================================
downloaded 427 KB


The downloaded binary packages are in
	/var/folders/sf/3lk5x37135586w0jgqyjq_yc0000gn/T//Rtmp1lPIZB/downloaded_packages
> require(devtools)
 要求されたパッケージ devtools をロード中です 
> install_version("RSQLite", version = "1.1-2", repos = "http://cran.us.r-project.org")
Downloading package from url: http://cran.us.r-project.org/src/contrib/Archive/RSQLite/RSQLite_1.1-2.tar.gz
Installing RSQLite
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/sf/3lk5x37135586w0jgqyjq_yc0000gn/T/Rtmp1lPIZB/devtoolsd810425d7aa4/RSQLite'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests 

* installing *source* package ‘RSQLite’ ...
**  パッケージ ‘RSQLite’ の解凍および MD5 サムの検証に成功しました 
** libs
Makevars:21: Makevars.local: No such file or directory
touch "Makevars.local"
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/plogr/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/plogr/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SqliteConnection.cpp -o SqliteConnection.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/plogr/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SqliteDataFrame.cpp -o SqliteDataFrame.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/plogr/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SqliteResult.cpp -o SqliteResult.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/plogr/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SqliteResultImpl.cpp -o SqliteResultImpl.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/plogr/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c affinity.c -o affinity.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/plogr/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c connection.cpp -o connection.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/plogr/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c import-file.c -o import-file.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/plogr/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c result.cpp -o result.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/plogr/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c rsqlite.cpp -o rsqlite.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/plogr/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c sqlite3/extension-functions.c -o sqlite3/extension-functions.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/plogr/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c sqlite3/sqlite3.c -o sqlite3/sqlite3.o
clang++ -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 RSQLite.so RcppExports.o SqliteConnection.o SqliteDataFrame.o SqliteResult.o SqliteResultImpl.o affinity.o connection.o import-file.o result.o rsqlite.o sqlite3/extension-functions.o sqlite3/sqlite3.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RSQLite/libs
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RSQLite)

これでいけるかと思ったが、やっぱり駄目だわ・。

同時にcummeRbundもバージョンアップされたかでRSQLite2.0を要求してくる。
で結局もとに戻ってしまう。