Closed TommyH-Tran closed 2 years ago
eead-csic-compbio
commented
2 years ago Please try to install cmake as suggested in the output :
CMake was not found on the PATH. Please install CMake:
sudo yum install cmake (Fedora/CentOS; inside a terminal)
sudo apt install cmake (Debian/Ubuntu; inside a terminal).
sudo pacman -S cmake (Arch Linux; inside a terminal).
sudo brew install cmake (MacOS; inside a terminal with Homebrew)
sudo port install cmake (MacOS; inside a terminal with MacPorts)Alternatively you can try the recently released package in bioconda, where the dependencies are already installed. See the instructions in the manual
TommyH-Tran
commented
2 years ago I did the cmake install using brew install make, however that did not completely fix the issue as "factoextra" package was still missing. I fixed this by trying to download it from a different region. There are 78 options and I choose 1: 0-Cloud [https] instead. I guess the location I was choosing was having problems sourcing the "factoextra" package. The option I was choosing before was 78: USA (TX 1) [https]. Guess that one is broken or something...
After, doing these two things I was able to get it working to generate the svg file. Thanks for the help!
I am trying to generate an ANI using the ANI .tab file. However, when I try to generate the .svg it seems to broken.
I am using the command:
./plot_matrix_heatmap.sh -i /Users/tommytran/Downloads/Cpr1274CJEI_f0_0taxa_CDS_algOMCL_e0_C90_Avg_identity.tab -d 2 -t "ALL CDS Cpr" -W 25 -H 30This is the output:
` plot_matrix_heatmap.sh vv1.0.4_31Jan18 run started at 2022_05_21-14.27.42 working directory : /Users/tommytran/get_homologues input tab_file : /Users/tommytran/Downloads/Cpr1274CJEI_f0_0taxa_CDS_algOMCL_e0_C90_Avg_identity.tab | sim_cutoff : 100 | max_decimals : 2 subset_matrix : 0 | regex : text:ALL CDS Cpr|margin_hor:18|margin_vert:18|points:15 angle:45|charExp:1.0|right_margin:10 width:25|height:30|outformat:svg reorder_clusters:1|remove_colnames:0|key_xaxis:Value|do_bioNJ:0 k:
Plotting file /Users/tommytran/Downloads/Cpr1274CJEI_f0_0taxa_CDS_algOMCL_e0_C90_Avg_identity_heatmap.svg Error in library(factoextra) : there is no package called ‘factoextra’ Calls: suppressPackageStartupMessages -> withCallingHandlers -> library Execution halted ERROR: file /Users/tommytran/Downloads/Cpr1274CJEI_f0_0taxa_CDS_algOMCL_e0_C90_Avg_identity_heatmap.svg was NOT produced.
You can try option -C or alternatively remove columns in the matrix.
file ANDg_meand_silhouette_width_statistic_plot.svg was produced
ERROR: file ./ANDg_hc_plot_cut_at_mean_silhouette_width_k5.svg ./ANDg_hc_plot_cut_at_mean_silhouette_width_k4.svg ./ANDg_hc_plot_cut_at_mean_silhouette_width_k3.svg ./ANDg_hc_plot_cut_at_mean_silhouette_width_k2.svg was NOT produced!
rm: Rplots.pdf: No such file or directory `
I had a it working about a week ago, and then I tried to install the package
factoextrasince it said It was missing then I got this output:1: 0-Cloud [https] 2: Australia (Canberra) [https] 3: Australia (Melbourne 1) [https] 4: Australia (Melbourne 2) [https] 5: Australia (Perth) [https] 6: Austria [https] 7: Belgium (Brussels) [https] 8: Brazil (PR) [https] 9: Brazil (RJ) [https] 10: Brazil (SP 1) [https] 11: Brazil (SP 2) [https] 12: Bulgaria [https] 13: Canada (MB) [https] 14: Canada (ON 3) [https] 15: Chile (Santiago) [https] 16: China (Beijing 2) [https] 17: China (Beijing 3) [https] 18: China (Hefei) [https] 19: China (Hong Kong) [https] 20: China (Guangzhou) [https] 21: China (Lanzhou) [https] 22: China (Nanjing) [https] 23: China (Shanghai 2) [https] 24: China (Shenzhen) [https] 25: Colombia (Cali) [https] 26: Costa Rica [https] 27: Cyprus [https] 28: Czech Republic [https] 29: Denmark [https] 30: East Asia [https] 31: Ecuador (Cuenca) [https] 32: Ecuador (Quito) [https] 33: Estonia [https] 34: France (Lyon 1) [https] 35: France (Lyon 2) [https] 36: France (Marseille) [https] 37: France (Paris 1) [https] 38: Germany (Erlangen) [https] 39: Germany (Leipzig) [https] 40: Germany (Göttingen) [https] 41: Germany (Münster) [https] 42: Germany (Regensburg) [https] 43: Greece [https] 44: Hungary [https] 45: Iceland [https] 46: Indonesia (Jakarta) [https] 47: Iran (Mashhad) [https] 48: Italy (Milano) [https] 49: Italy (Padua) [https] 50: Japan (Tokyo) [https] 51: Korea (Gyeongsan-si) [https] 52: Korea (Seoul 1) [https] 53: Korea (Ulsan) [https] 54: Malaysia [https] 55: Mexico (Mexico City) [https] 56: Morocco [https] 57: Netherlands [https] 58: New Zealand [https] 59: Norway [https] 60: South Africa (Johannesburg) [https] 61: Spain (A Coruña) [https] 62: Spain (Madrid) [https] 63: Sweden (Borås) [https] 64: Sweden (Umeå) [https] 65: Switzerland [https] 66: Taiwan (Taipei) [https] 67: Turkey (Denizli) [https] 68: Turkey (Istanbul) [https] 69: Turkey (Mersin) [https] 70: UK (Bristol) [https] 71: UK (London 1) [https] 72: USA (IA) [https] 73: USA (KS) [https] 74: USA (MI) [https] 75: USA (OH) [https] 76: USA (OR) [https] 77: USA (TN) [https] 78: USA (TX 1) [https] 79: Uruguay [https] 80: (other mirrors)
Selection: 78 also installing the dependencies ‘nloptr’, ‘pbkrtest’, ‘lme4’, ‘car’, ‘rstatix’, ‘FactoMineR’, ‘ggpubr’
trying URL 'https://cran.microsoft.com/src/contrib/nloptr_2.0.2.tar.gz' Content type 'application/octet-stream' length 2219995 bytes (2.1 MB) downloaded 2.1 MB
trying URL 'https://cran.microsoft.com/src/contrib/pbkrtest_0.5.1.tar.gz' Content type 'application/octet-stream' length 246327 bytes (240 KB) downloaded 240 KB
trying URL 'https://cran.microsoft.com/src/contrib/lme4_1.1-29.tar.gz' Content type 'application/octet-stream' length 3306026 bytes (3.2 MB) downloaded 3.2 MB
trying URL 'https://cran.microsoft.com/src/contrib/car_3.0-13.tar.gz' Content type 'application/octet-stream' length 494341 bytes (482 KB) downloaded 482 KB
trying URL 'https://cran.microsoft.com/src/contrib/rstatix_0.7.0.tar.gz' Content type 'application/octet-stream' length 402481 bytes (393 KB) downloaded 393 KB
trying URL 'https://cran.microsoft.com/src/contrib/FactoMineR_2.4.tar.gz' Content type 'application/octet-stream' length 2822993 bytes (2.7 MB) downloaded 2.7 MB
trying URL 'https://cran.microsoft.com/src/contrib/ggpubr_0.4.0.tar.gz' Content type 'application/octet-stream' length 2689307 bytes (2.6 MB) downloaded 2.6 MB
trying URL 'https://cran.microsoft.com/src/contrib/factoextra_1.0.7.tar.gz' Content type 'application/octet-stream' length 1386480 bytes (1.3 MB) downloaded 1.3 MB
------------------ CMAKE NOT FOUND --------------------
CMake was not found on the PATH. Please install CMake:
Alternatively install CMake from: https://cmake.org/
ERROR: configuration failed for package ‘nloptr’
The downloaded source packages are in ‘/private/var/folders/_y/j9xb7x3s3c7cz22lldv6rmd40000gn/T/RtmpbHD5yG/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning messages: 1: In install.packages("factoextra") : installation of package ‘nloptr’ had non-zero exit status 2: In install.packages("factoextra") : installation of package ‘lme4’ had non-zero exit status 3: In install.packages("factoextra") : installation of package ‘pbkrtest’ had non-zero exit status 4: In install.packages("factoextra") : installation of package ‘car’ had non-zero exit status 5: In install.packages("factoextra") : installation of package ‘rstatix’ had non-zero exit status 6: In install.packages("factoextra") : installation of package ‘FactoMineR’ had non-zero exit status 7: In install.packages("factoextra") : installation of package ‘ggpubr’ had non-zero exit status 8: In install.packages("factoextra") : installation of package ‘factoextra’ had non-zero exit status