5 Bioconductor包安装时出现警告，导致最后出来的图片部分缺失
教程中推荐安装步骤
Bioconductor包安装
R source("http://bioconductor.org/biocLite.R") biocLite(c("genefilter","ballgown","edgeR")) quit(save="no")
紧接着跑差异分析
echo "Step8: difference expression analysis "
cd /var/data/work/
DE_HTSEQ=/var/data/work/5.de
mkdir -p /var/data/work/5.de
cd /var/data/work/5.de
perl -ne 'if ($_ =~ /gene_id\s\"(ENSG\S+)\"\;/) { $id = $1; $name = undef; if ($_ =~ /gene_name\s\"(\S+)"\;/) { $name = $1; }; }; if ($id && $name) {print "$id\t$name\n";} if ($_=~/gene_id\s\"(ERCC\S+)\"/){print "$1\t$1\n";}' /var/data/work/refs/chr22_with_ERCC92.gtf | sort | uniq > ENSG_ID2Name.txt
head ENSG_ID2Name.txt
Rscript /var/data/demo/script/edgeR_deg.R /var/data/work/5.de /var/data/work/4.expression/gene_read_counts_table_all_final.tsv
出来的结果如图：
缺少上下调的变化，返回看edgeR等安装步骤发现了如下几个警告：
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
> biocLite(c("genefilter","ballgown","edgeR"))
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).
Installing package(s) ‘genefilter’, ‘ballgown’, ‘edgeR’
also installing the dependencies ‘AnnotationDbi’, ‘annotate’, ‘sva’
trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/AnnotationDbi_1.32.3.tar.gz'
Content type 'application/x-gzip' length 4268480 bytes (4.1 MB)
==================================================
downloaded 4.1 MB
trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/annotate_1.48.0.tar.gz'
Content type 'application/x-gzip' length 1852419 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/sva_3.18.0.tar.gz'
Content type 'application/x-gzip' length 197650 bytes (193 KB)
==================================================
downloaded 193 KB
trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/genefilter_1.52.1.tar.gz'
Content type 'application/x-gzip' length 1290725 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/ballgown_2.2.0.tar.gz'
Content type 'application/x-gzip' length 2972831 bytes (2.8 MB)
==================================================
downloaded 2.8 MB
trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/edgeR_3.12.1.tar.gz'
Content type 'application/x-gzip' length 1193464 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘DBI’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
Warning: S3 method ‘format.SQLiteConnection’ was declared in NAMESPACE but not found
Error in library.dynam(lib, package, package.lib) :
shared object ‘RSQLite.so’ not found
ERROR: lazy loading failed for package ‘AnnotationDbi’
* removing ‘/usr/local/lib/R/site-library/AnnotationDbi’
* installing *source* package ‘edgeR’ ...
** libs
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_compute_nbdev.cpp -o R_compute_nbdev.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_levenberg.cpp -o R_levenberg.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_loess_by_col.cpp -o R_loess_by_col.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_one_group.cpp -o R_one_group.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c adj_coxreid.cpp -o adj_coxreid.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fmm_spline.c -o fmm_spline.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c glm_levenberg.cpp -o glm_levenberg.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c glm_one_group.cpp -o glm_one_group.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.cpp -o init.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c interpolator.cpp -o interpolator.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c matvec_check.cpp -o matvec_check.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nbdev.cpp -o nbdev.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o edgeR.so R_compute_nbdev.o R_cr_adjust.o R_exact_test_by_deviance.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/edgeR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (edgeR)
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘annotate’
* removing ‘/usr/local/lib/R/site-library/annotate’
ERROR: dependencies ‘AnnotationDbi’, ‘annotate’ are not available for package ‘genefilter’
* removing ‘/usr/local/lib/R/site-library/genefilter’
ERROR: dependency ‘genefilter’ is not available for package ‘sva’
* removing ‘/usr/local/lib/R/site-library/sva’
ERROR: dependency ‘sva’ is not available for package ‘ballgown’
* removing ‘/usr/local/lib/R/site-library/ballgown’
The downloaded source packages are in
‘/tmp/RtmphUj100/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘AnnotationDbi’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘sva’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘ballgown’ had non-zero exit status
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