Wei Shi
| Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024) |
| git_url: https://git.bioconductor.org/packages/Rsubread |
| git_branch: RELEASE_3_19 |
| git_last_commit: 900c360 |
| git_last_commit_date: 2024-04-30 10:23:58 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:41:23 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 | ||||
| Package 1828/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsubread 2.18.0 (landing page) Wei Shi
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the Rsubread package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rsubread.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Rsubread |
| Version: 2.18.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL Rsubread |
| StartedAt: 2024-05-08 20:02:51 -0000 (Wed, 08 May 2024) |
| EndedAt: 2024-05-08 20:03:49 -0000 (Wed, 08 May 2024) |
| EllapsedTime: 57.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL Rsubread
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ The operating system is Linux.
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c HelperFunctions.c -o HelperFunctions.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c LRMbase-index.c -o LRMbase-index.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c LRMchro-event.c -o LRMchro-event.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c LRMfile-io.c -o LRMfile-io.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c LRMhashtable.c -o LRMhashtable.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c LRMhelper.c -o LRMhelper.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c R_wrapper.c -o R_wrapper.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c RsimReads.c -o RsimReads.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c SNPCalling.c -o SNPCalling.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c aligner.c -o aligner.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c atgcContent.c -o atgcContent.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c build-sam-index.c -o build-sam-index.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c cell-counts.c -o cell-counts.o
cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’:
cell-counts.c:1621:5: warning: ‘search_start’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1621 | if(search_start>0xffffff00) return;
| ^
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c core-bigtable.c -o core-bigtable.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c core-indel.c -o core-indel.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c core-interface-aligner.c -o core-interface-aligner.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c core-junction.c -o core-junction.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c core.c -o core.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c detection-calls.c -o detection-calls.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c detectionCall.c -o detectionCall.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c exon-algorithms.c -o exon-algorithms.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c exon-align-indel.c -o exon-align-indel.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c exon-align.c -o exon-align.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c flattenAnnotations.c -o flattenAnnotations.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c fullscan.c -o fullscan.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c fusion-align.c -o fusion-align.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c gen_rand_reads.c -o gen_rand_reads.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c gene-algorithms.c -o gene-algorithms.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c gene-value-index.c -o gene-value-index.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c hashtable.c -o hashtable.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c index-builder.c -o index-builder.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c input-blc.c -o input-blc.o
input-blc.c: In function ‘iCache_continuous_read_lanes’:
input-blc.c:580:17: warning: unused variable ‘npos’ [-Wunused-variable]
580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
| ^~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c input-files.c -o input-files.o
input-files.c: In function ‘reduce_SAM_to_BAM’:
input-files.c:3242:6: warning: unused variable ‘seq_len’ [-Wunused-variable]
3242 | int seq_len = qual - seq - 1;
| ^~~~~~~
input-files.c: In function ‘SAM_pairer_fix_format’:
input-files.c:4832:43: warning: variable ‘readname’ set but not used [-Wunused-but-set-variable]
4832 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256];
| ^~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c interval_merge.c -o interval_merge.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c long-hashtable.c -o long-hashtable.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c longread-mapping.c -o longread-mapping.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c mergeVCF.c -o mergeVCF.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c processExons.c -o processExons.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c propmapped.c -o propmapped.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c qualityScores.c -o qualityScores.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c read-repair.c -o read-repair.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c readSummary.c -o readSummary.o
readSummary.c: In function ‘vote_and_add_count’:
readSummary.c:3804:16: warning: variable ‘assignment_target_number’ set but not used [-Wunused-but-set-variable]
3804 | srInt_64 assignment_target_number = tmp_voter_id;
| ^~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function ‘fc_thread_merge_results’:
readSummary.c:3874:25: warning: unused variable ‘sample_i’ [-Wunused-variable]
3874 | int xk1, xk2, ret = 0, sample_i;
| ^~~~~~~~
readSummary.c: In function ‘readSummary’:
readSummary.c:5635:45: warning: variable ‘scrna_total_BAM_no’ set but not used [-Wunused-but-set-variable]
5635 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no;
| ^~~~~~~~~~~~~~~~~~
readSummary.c: In function ‘vote_and_add_count’:
readSummary.c:3737:31: warning: ‘longest_overlap_score’ may be used uninitialized in this function [-Wmaybe-uninitialized]
3737 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0;
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c removeDupReads.c -o removeDupReads.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c sam2bed.c -o sam2bed.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c sambam-file.c -o sambam-file.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c seek-zlib.c -o seek-zlib.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c sorted-hashtable.c -o sorted-hashtable.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c sublog.c -o sublog.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.18.0\"" -fPIC -g -O2 -Wall -c tx-unique.c -o tx-unique.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rsubread/00new/Rsubread/libs
** R
** 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 (Rsubread)