installation error

[crazyhottommy]

Hi,

I got the error below.

* installing *source* package ‘alevinQC’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  namespace ‘tximport’ 1.10.1 is being loaded, but >= 1.11.5 is required
ERROR: lazy loading failed for package ‘alevinQC’
* removing ‘/n/home02/mtang/R-3.5-lib/alevinQC’
Error in i.p(...) :
  (converted from warning) installation of package ‘/tmp/Rtmp2xcKTi/filebd6615864377/alevinQC_0.1.2.tar.gz’ had non-zero exit status

devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 3.5.1 (2018-07-02)
 os       CentOS Linux 7 (Core)
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       EST5EDT,M3.2.0,M11.1.0
 date     2019-01-22

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version date       lib source
 assertthat    0.2.0   2017-04-11 [2] CRAN (R 3.5.1)
 backports     1.1.2   2017-12-13 [2] CRAN (R 3.5.1)
 base64enc     0.1-3   2015-07-28 [2] CRAN (R 3.5.1)
 BiocManager   1.30.4  2018-11-13 [1] CRAN (R 3.5.1)
 callr         3.0.0   2018-08-24 [2] CRAN (R 3.5.1)
 cli           1.0.1   2018-09-25 [2] CRAN (R 3.5.1)
 crayon        1.3.4   2017-09-16 [2] CRAN (R 3.5.1)
 curl          3.2     2018-03-28 [2] CRAN (R 3.5.1)
 desc          1.2.0   2018-05-01 [1] CRAN (R 3.5.1)
 devtools      2.0.1   2018-10-26 [1] CRAN (R 3.5.1)
 digest        0.6.17  2018-09-12 [2] CRAN (R 3.5.1)
 fs            1.2.6   2018-08-23 [1] CRAN (R 3.5.1)
 glue          1.3.0   2018-07-17 [2] CRAN (R 3.5.1)
 magrittr      1.5     2014-11-22 [2] CRAN (R 3.5.1)
 memoise       1.1.0   2017-04-21 [2] CRAN (R 3.5.1)
 pkgbuild      1.0.2   2018-10-16 [1] CRAN (R 3.5.1)
 pkgload       1.0.2   2018-10-29 [1] CRAN (R 3.5.1)
 prettyunits   1.0.2   2015-07-13 [2] CRAN (R 3.5.1)
 processx      3.2.0   2018-08-16 [2] CRAN (R 3.5.1)
 ps            1.1.0   2018-08-10 [2] CRAN (R 3.5.1)
 R6            2.3.0   2018-10-04 [2] CRAN (R 3.5.1)
 Rcpp          0.12.19 2018-10-01 [2] CRAN (R 3.5.1)
 remotes       2.0.2   2018-10-30 [1] CRAN (R 3.5.1)
 rlang         0.3.0.1 2018-10-25 [1] CRAN (R 3.5.1)
 rprojroot     1.3-2   2018-01-03 [1] CRAN (R 3.5.1)
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 3.5.1)
 usethis       1.4.0   2018-08-14 [1] CRAN (R 3.5.1)
 withr         2.1.2   2018-03-15 [2] CRAN (R 3.5.1)

[1] /n/home02/mtang/R-3.5-lib
[2] /n/sw/helmod/apps/centos7/Core/R_packages/3.5.1-fasrc01
[3] /n/sw/helmod/apps/centos7/Core/R_core/3.5.1-fasrc01/lib64/R/library
[4] /n/sw/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/R_packages/3.5.1-fasrc02
[5] /n/sw/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/R_core/3.5.1-fasrc02/lib64/R/library
>
[ bioinf01 | 12.86 10.27 5.46 ][                                (1*$bash)  3$ bash  4$ bash  5$ bash  6$ bash  7-$ bash                                ][ 22/01 10:39 ]
 date     2019-01-22

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version date       lib source
 assertthat    0.2.0   2017-04-11 [2] CRAN (R 3.5.1)
 backports     1.1.2   2017-12-13 [2] CRAN (R 3.5.1)
 base64enc     0.1-3   2015-07-28 [2] CRAN (R 3.5.1)
 BiocManager   1.30.4  2018-11-13 [1] CRAN (R 3.5.1)
 callr         3.0.0   2018-08-24 [2] CRAN (R 3.5.1)
 cli           1.0.1   2018-09-25 [2] CRAN (R 3.5.1)
 crayon        1.3.4   2017-09-16 [2] CRAN (R 3.5.1)
 curl          3.2     2018-03-28 [2] CRAN (R 3.5.1)
 desc          1.2.0   2018-05-01 [1] CRAN (R 3.5.1)
 devtools      2.0.1   2018-10-26 [1] CRAN (R 3.5.1)
 digest        0.6.17  2018-09-12 [2] CRAN (R 3.5.1)
 fs            1.2.6   2018-08-23 [1] CRAN (R 3.5.1)
 glue          1.3.0   2018-07-17 [2] CRAN (R 3.5.1)
 magrittr      1.5     2014-11-22 [2] CRAN (R 3.5.1)
 memoise       1.1.0   2017-04-21 [2] CRAN (R 3.5.1)
 pkgbuild      1.0.2   2018-10-16 [1] CRAN (R 3.5.1)
 pkgload       1.0.2   2018-10-29 [1] CRAN (R 3.5.1)
 prettyunits   1.0.2   2015-07-13 [2] CRAN (R 3.5.1)
 processx      3.2.0   2018-08-16 [2] CRAN (R 3.5.1)
 ps            1.1.0   2018-08-10 [2] CRAN (R 3.5.1)
 R6            2.3.0   2018-10-04 [2] CRAN (R 3.5.1)
 Rcpp          0.12.19 2018-10-01 [2] CRAN (R 3.5.1)
 remotes       2.0.2   2018-10-30 [1] CRAN (R 3.5.1)
 rlang         0.3.0.1 2018-10-25 [1] CRAN (R 3.5.1)
 rprojroot     1.3-2   2018-01-03 [1] CRAN (R 3.5.1)
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 3.5.1)
 usethis       1.4.0   2018-08-14 [1] CRAN (R 3.5.1)
 withr         2.1.2   2018-03-15 [2] CRAN (R 3.5.1)

[1] /n/home02/mtang/R-3.5-lib
[2] /n/sw/helmod/apps/centos7/Core/R_packages/3.5.1-fasrc01
[3] /n/sw/helmod/apps/centos7/Core/R_core/3.5.1-fasrc01/lib64/R/library
[4] /n/sw/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/R_packages/3.5.1-fasrc02
[5] /n/sw/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/R_core/3.5.1-fasrc02/lib64/R/library

I installed the tximport separately using

BiocManager::install("tximport", version = "3.8")

and repeat the installation of alevinQC, still failed.

Thanks!

[csoneson]

Currently you need to have the development version of tximport (and thus, the devel version of Bioconductor) for alevinQC to work (as indicated in the error message, tximport version >=1.11.5 is required), since this is where the code to import the alevin quantifications was introduced.

[crazyhottommy]

thanks!