installation failed: SummarizedExperiment

[metalichen]

Hi there,

I'm getting an error while trying to install the package. Below is the output when I try to install the lite version, but I get the same error with the /powsimR@HEAD. Here is what I get if I select to skip updating SummarizedExperiment:

> remotes::install_github("bvieth/powsimR", ref = "lite", dependencies = TRUE, upgrade = "ask")
Downloading GitHub repo bvieth/powsimR@lite
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                                         
2: CRAN packages only                          
3: None                                        
4: DESeq2       (1.34.0 -> 17a39b529...) [Bioc]
5: Summarize... (1.24.0 -> fbea511b8...) [Bioc]

Enter one or more numbers, or an empty line to skip updates: 2
── R CMD build ────────────────────────────────────────
✔  checking for file ‘/private/var/folders/nz/wc3s4mdn3450y_pt54pmh1cr000fqh/T/Rtmp6Dkmrj/remotesea66665f3892/bvieth-powsimR-827f491/DESCRIPTION’ ...
─  preparing ‘powsimR’:
✔  checking DESCRIPTION meta-information ...
─  excluding invalid files
   Subdirectory 'R' contains invalid file names:
     ‘_description-lite.R’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘powsimR_0.0.900.tar.gz’
   Warning in sprintf(gettext(fmt, domain = domain), ...) :
     one argument not used by format 'invalid gid value replaced by that for user 'nobody''
   Warning: invalid gid value replaced by that for user 'nobody'
   
* installing *source* package ‘powsimR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: multiple methods tables found for ‘aperm’
Warning: replacing previous import ‘BiocGenerics::aperm’ by ‘DelayedArray::aperm’ when loading ‘SummarizedExperiment’
Error: objects ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ are not exported by 'namespace:BiocGenerics'
Execution halted
ERROR: lazy loading failed for package ‘powsimR’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/powsimR’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/nz/wc3s4mdn3450y_pt54pmh1cr000fqh/T//Rtmp6Dkmrj/fileea66ec47625/powsimR_0.0.900.tar.gz’ had non-zero exit status

Here, if I select to update SummarizedExperiment:

remotes::install_github("bvieth/powsimR", ref = "lite", dependencies = TRUE, upgrade = "ask")
Downloading GitHub repo bvieth/powsimR@lite
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                                         
2: CRAN packages only                          
3: None                                        
4: DESeq2       (1.34.0 -> 17a39b529...) [Bioc]
5: Summarize... (1.24.0 -> fbea511b8...) [Bioc]

Enter one or more numbers, or an empty line to skip updates: 1
DESeq2       (1.34.0 -> 17a39b529...) [Bioc]
Summarize... (1.24.0 -> fbea511b8...) [Bioc]
Skipping 1 packages not available: BiocStyle
Downloading Bioconductor repo https://git.bioconductor.org/packages/DESeq2
'/usr/bin/git' clone --depth 1 --no-hardlinks --branch RELEASE_3_18 https://git.bioconductor.org/packages/DESeq2 /var/folders/nz/wc3s4mdn3450y_pt54pmh1cr000fqh/T//Rtmp6Dkmrj/fileea6644a9decf
Cloning into '/var/folders/nz/wc3s4mdn3450y_pt54pmh1cr000fqh/T//Rtmp6Dkmrj/fileea6644a9decf'...
── R CMD build ────────────────────────────────────────
✔  checking for file ‘/private/var/folders/nz/wc3s4mdn3450y_pt54pmh1cr000fqh/T/Rtmp6Dkmrj/fileea6644a9decf/DESCRIPTION’ ...
─  preparing ‘DESeq2’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘DESeq2_1.42.0.tar.gz’
   Warning in sprintf(gettext(fmt, domain = domain), ...) :
     one argument not used by format 'invalid gid value replaced by that for user 'nobody''
   Warning: invalid gid value replaced by that for user 'nobody'
   
* installing *source* package ‘DESeq2’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c DESeq2.cpp -o DESeq2.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 DESeq2.so DESeq2.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/current/ -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-DESeq2/00new/DESeq2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: multiple methods tables found for ‘aperm’ 
2: replacing previous import ‘BiocGenerics::aperm’ by ‘DelayedArray::aperm’ when loading ‘SummarizedExperiment’ 
Error: object ‘colMeans’ is not exported by 'namespace:MatrixGenerics'
Execution halted
ERROR: lazy loading failed for package ‘DESeq2’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/DESeq2’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/DESeq2’
Downloading Bioconductor repo https://git.bioconductor.org/packages/SummarizedExperiment
'/usr/bin/git' clone --depth 1 --no-hardlinks --branch RELEASE_3_18 https://git.bioconductor.org/packages/SummarizedExperiment /var/folders/nz/wc3s4mdn3450y_pt54pmh1cr000fqh/T//Rtmp6Dkmrj/fileea66471d44bf
Cloning into '/var/folders/nz/wc3s4mdn3450y_pt54pmh1cr000fqh/T//Rtmp6Dkmrj/fileea66471d44bf'...
Skipping 1 packages not available: S4Arrays
── R CMD build ────────────────────────────────────────
✔  checking for file ‘/private/var/folders/nz/wc3s4mdn3450y_pt54pmh1cr000fqh/T/Rtmp6Dkmrj/fileea66471d44bf/DESCRIPTION’ ...
─  preparing ‘SummarizedExperiment’: (437ms)
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘SummarizedExperiment_1.32.0.tar.gz’
   Warning in sprintf(gettext(fmt, domain = domain), ...) :
     one argument not used by format 'invalid gid value replaced by that for user 'nobody''
   Warning: invalid gid value replaced by that for user 'nobody'
   
ERROR: dependency ‘S4Arrays’ is not available for package ‘SummarizedExperiment’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/SummarizedExperiment’
── R CMD build ────────────────────────────────────────
✔  checking for file ‘/private/var/folders/nz/wc3s4mdn3450y_pt54pmh1cr000fqh/T/Rtmp6Dkmrj/remotesea666e8ea02a/bvieth-powsimR-827f491/DESCRIPTION’ ...
─  preparing ‘powsimR’:
✔  checking DESCRIPTION meta-information ...
─  excluding invalid files
   Subdirectory 'R' contains invalid file names:
     ‘_description-lite.R’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘powsimR_0.0.900.tar.gz’
   Warning in sprintf(gettext(fmt, domain = domain), ...) :
     one argument not used by format 'invalid gid value replaced by that for user 'nobody''
   Warning: invalid gid value replaced by that for user 'nobody'
   
ERROR: dependency ‘SummarizedExperiment’ is not available for package ‘powsimR’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/powsimR’
Warning messages:
1: In i.p(...) :
  installation of package ‘/var/folders/nz/wc3s4mdn3450y_pt54pmh1cr000fqh/T//Rtmp6Dkmrj/fileea666030c25c/DESeq2_1.42.0.tar.gz’ had non-zero exit status
2: In i.p(...) :
  installation of package ‘/var/folders/nz/wc3s4mdn3450y_pt54pmh1cr000fqh/T//Rtmp6Dkmrj/fileea66528c7c12/SummarizedExperiment_1.32.0.tar.gz’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘/var/folders/nz/wc3s4mdn3450y_pt54pmh1cr000fqh/T//Rtmp6Dkmrj/fileea666eb4ff40/powsimR_0.0.900.tar.gz’ had non-zero exit status

Here, it seems the problem is that I can't install S4Arrays because I have an older version of Bioconductor (3.14), and I can't update to 3.18 unless I update my R to 4.3, and I don't want to do it because some of the libraries I'm working with might not have a build compatible with 4.3 yet.

Is there a way to install powsimR without updating my R?

These are versions of dependencies:

> ip.check
                Package Version
1                 broom   1.0.5
2                  cobs   1.3-5
3               cowplot   1.1.1
4            data.table  1.14.8
5            doParallel  1.0.17
6                 dplyr   1.1.3
7              DrImpute     1.0
8               fastICA   1.2-3
9          fitdistrplus  1.1-11
10              foreach   1.5.2
11               future  1.33.0
12          gamlss.dist   6.1-1
13              ggplot2   3.4.4
14               ggpubr   0.6.0
15             ggstance   0.3.6
16            grDevices   4.1.2
17                 grid   4.1.2
18                Hmisc   5.1-1
19              kernlab  0.9-32
20                 MASS  7.3-60
21             magrittr   2.0.3
22                MBESS   4.9.3
23               Matrix 1.6-1.1
24          matrixStats   1.1.0
25               mclust   6.0.1
26              methods   4.1.2
27           minpack.lm   1.2-4
28              moments  0.14.1
29                 msir   1.3.3
30               NBPSeq   0.3.1
31             nonnest2   0.5-6
32             parallel   4.1.2
33            penalized  0.9-52
34                 plyr   1.8.9
35                 pscl 1.5.5.1
36             reshape2   1.4.4
37               Rmagic   2.0.3
38                 rsvd   1.0.5
39                Rtsne    0.16
40               scales   1.2.1
41               Seurat   5.0.0
42                 snow   0.4-4
43          sctransform   0.4.1
44                stats   4.1.2
45               tibble   3.2.1
46                tidyr   1.3.0
47            truncnorm   1.0-9
48                 VGAM   1.1-9
49                  ZIM   1.1.0
50                  zoo  1.8-12
51              bayNorm  1.20.0
52               baySeq  2.36.0
53         BiocGenerics  0.48.1
54         BiocParallel  1.36.0
55               DESeq2  1.34.0
56                EBSeq   2.0.0
57                edgeR   4.0.1
58                  IHW  1.30.0
59               iCOBRA  1.30.0
60                limma  3.58.1
61              Linnorm  2.26.0
62                 MAST  1.28.0
63              monocle  2.30.0
64               NOISeq  2.46.0
65               qvalue  2.34.0
66                 ROTS  1.30.0
67               RUVSeq  1.36.0
68            S4Vectors  0.40.1
69               scater  1.30.1
70                 scDD  1.26.0
71                 scde  2.30.0
72                scone  1.26.0
73                scran  1.30.0
74               SCnorm  1.23.0
75 SingleCellExperiment  1.24.0
76 SummarizedExperiment  1.24.0
77             zinbwave  1.16.0
78               DECENT   1.1.1
79                 BPSC  0.99.2
80                SAVER   1.1.3
81               zingeR   0.1.0
82             scImpute   0.0.9

This is the session info

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 13.3.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets 
[6] methods   base     

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0    remotes_2.4.2.1    
 [3] purrr_1.0.2         rhdf5_2.38.1       
 [5] colorspace_2.1-0    vctrs_0.6.4        
 [7] generics_0.1.3      usethis_2.2.2      
 [9] miniUI_0.1.1.1      htmltools_0.5.7    
[11] utf8_1.2.4          rlang_1.1.2        
[13] pkgbuild_1.4.2      urlchecker_1.0.1   
[15] pillar_1.9.0        later_1.3.1        
[17] glue_1.6.2          sleuth_0.30.1      
[19] sessioninfo_1.2.2   lifecycle_1.0.4    
[21] stringr_1.5.1       munsell_0.5.0      
[23] gtable_0.3.4        devtools_2.4.5     
[25] htmlwidgets_1.6.2   memoise_2.0.1      
[27] callr_3.7.3         fastmap_1.1.1      
[29] httpuv_1.6.12       ps_1.7.5           
[31] curl_5.1.0          fansi_1.0.5        
[33] Rcpp_1.0.11         xtable_1.8-4       
[35] BiocManager_1.30.22 scales_1.2.1       
[37] promises_1.2.1      cachem_1.0.8       
[39] desc_1.4.2          pkgload_1.3.3      
[41] mime_0.12           fs_1.6.3           
[43] ggplot2_3.4.4       digest_0.6.33      
[45] stringi_1.8.1       processx_3.8.2     
[47] dplyr_1.1.3         shiny_1.7.5.1      
[49] grid_4.1.2          rprojroot_2.0.4    
[51] cli_3.6.1           tools_4.1.2        
[53] rhdf5filters_1.6.0  magrittr_2.0.3     
[55] lazyeval_0.2.2      tibble_3.2.1       
[57] profvis_0.3.8       crayon_1.5.2       
[59] pkgconfig_2.0.3     ellipsis_0.3.2     
[61] data.table_1.14.8   prettyunits_1.2.0  
[63] rstudioapi_0.15.0   Rhdf5lib_1.16.0    
[65] R6_2.5.1            compiler_4.1.2 

Thank you!

[zeyan-0717]

I met with similar problem, too! I have updated dependencies but it seems to enter a weird loop, i.e., the updating processes never end and repeated over and over again. so I failed to install the package at a very beginning.