===============================
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
--2023-10-20 17:45:52-- 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
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% 55.6M=0s
2023-10-20 17:45:58 (55.6 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
===============================
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
--2023-10-20 17:47:10-- 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)... 130.14.250.12, 165.112.9.228, 2607:f220:41e:250::13, ...
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.12|: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% 157M=0s
2023-10-20 17:47:10 (157 MB/s) - ‘GSE121810_series_matrix.txt.gz’ saved [3326/3326]
trying URL '/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip'
trying URL '/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip'
--2023-10-20 17:49:57-- 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, 130.14.250.12, 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: 15160 (15K) [application/x-gzip]
Saving to: ‘GSE58135_series_matrix.txt.gz’
0K .......... .... 100% 1.26M=0.01s
2023-10-20 17:49:58 (1.26 MB/s) - ‘GSE58135_series_matrix.txt.gz’ saved [15160/15160]
Quitting from lines 639-646 [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