===============================
R CMD BUILD
===============================
* checking for file ‘SurfR/DESCRIPTION’ ... OK
* preparing ‘SurfR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Intro_to_SurfR.Rmd’ using rmarkdown
--2023-10-21 14:51:52-- https://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121810/matrix/GSE121810_series_matrix.txt.gz
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 165.112.9.228, 165.112.9.230, 2607:f220:41f:250::229, ...
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|165.112.9.228|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3326 (3.2K) [application/x-gzip]
Saving to: ‘GSE121810_series_matrix.txt.gz’
0K ... 100% 189M=0s
2023-10-21 14:51:52 (189 MB/s) - ‘GSE121810_series_matrix.txt.gz’ saved [3326/3326]
trying URL '/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip'
/usr/bin/tar: MANIFEST.txt: time stamp 2023-10-21 14:53:20.7368822 is 6.716592292 s in the future
/usr/bin/tar: 248ac510-a5af-4608-9cdc-5c8673633b82/d23ff3bc-5524-4dca-b0f4-a1561a30566c.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-21 14:53:20.7372563 is 6.687003613 s in the future
/usr/bin/tar: 4df2233b-3bbc-4d20-9abc-2a09b3f37383/eb0f8bc7-5f47-4174-8e85-678bd011bc3c.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-21 14:53:21.185623 is 7.105755605 s in the future
/usr/bin/tar: 6b62d6dd-bb6f-4f39-9041-992c47b875f3/d1f7678a-8106-46c9-95b7-5ec5d940f08c.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-21 14:53:21.639096 is 7.530172801 s in the future
/usr/bin/tar: 90eefb33-6808-45c3-9ab1-6eca0decdc9d/71c9a6fc-0538-4533-af51-f7c9defe7770.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-21 14:53:22.099673 is 7.961827474 s in the future
/usr/bin/tar: eddb2dc6-2b72-43a8-a7fc-3dd09dde68af/316d8a79-9084-4355-9de7-e29503bf0864.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-21 14:53:22.5652592 is 8.398248822 s in the future
/usr/bin/tar: f66aace4-01a4-4def-8e71-26d9aaf13d49/9db2f825-0d02-4437-9107-a6b92ef4e2cc.rna_seq.augmented_star_gene_counts.tsv: time stamp 2023-10-21 14:53:23.0292523 is 8.833226713 s in the future
--2023-10-21 14:53:16-- https://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58135/matrix/GSE58135_series_matrix.txt.gz
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 165.112.9.228, 165.112.9.230, 2607:f220:41f:250::230, ...
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|165.112.9.228|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 15160 (15K) [application/x-gzip]
Saving to: ‘GSE58135_series_matrix.txt.gz’
0K .......... .... 100% 1.20M=0.01s
2023-10-21 14:53:16 (1.20 MB/s) - ‘GSE58135_series_matrix.txt.gz’ saved [15160/15160]
Quitting from lines 616-623 [unnamed-chunk-11] (Intro_to_SurfR.Rmd)
Error: processing vignette 'Intro_to_SurfR.Rmd' failed with diagnostics:
unable to find an inherited method for function 'plotPCA' for signature '"missing"'
--- failed re-building ‘Intro_to_SurfR.Rmd’
SUMMARY: processing the following file failed:
‘Intro_to_SurfR.Rmd’
Error: Vignette re-building failed.
Execution halted
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R CMD BUILD
===============================
* checking for file ‘SurfR/DESCRIPTION’ ... OK
* preparing ‘SurfR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Intro_to_SurfR.Rmd’ using rmarkdown
--2023-10-21 14:51:20-- https://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121810/matrix/GSE121810_series_matrix.txt.gz
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.7, 165.112.9.229
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.7|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3326 (3.2K) [application/x-gzip]
Saving to: ‘GSE121810_series_matrix.txt.gz’
0K ... 100% 83.5M=0s
2023-10-21 14:51:26 (83.5 MB/s) - ‘GSE121810_series_matrix.txt.gz’ saved [3326/3326]
Quitting from lines 183-211 [GEO input] (Intro_to_SurfR.Rmd)
Error: processing vignette 'Intro_to_SurfR.Rmd' failed with diagnostics:
Rhdf5lib was not compiled with support for the S3 VFD
--- failed re-building ‘Intro_to_SurfR.Rmd’
SUMMARY: processing the following file failed:
‘Intro_to_SurfR.Rmd’
Error: Vignette re-building failed.
Execution halted