!System command 'Rcmd.exe' failed

[chongchunwie]

Describe the Installation Issue
I am facing the following installation issue

Error Messages
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\LENOVO\AppData\Local\Temp\RtmpOOzPsy\remotes94546abe4490\cafferychen777-MicrobiomeStat-0ccb605/DESCRIPTION'
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_areaplot_pair_subject_subject_id_time_visit_number_num_feature_level_Family_feature_number_20_group_sample_body_site_strata_subject_race_avergae.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_areaplot_pair_subject_subject_id_time_visit_number_num_feature_level_Family_feature_number_20_group_sample_body_site_strata_subject_race_avergae.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_barplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_feature_number_20_group_sample_body_site_strata_subject_race_avergae.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_barplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_feature_number_20_group_sample_body_site_strata_subject_race_avergae.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_boxplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_sample_body_site_strata_subject_race_Family.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_boxplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_sample_body_site_strata_subject_race_Family.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_boxplot_single_subject_subject.id_feature_level_Family_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_antiexposedall_strata_delivery_Family.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_boxplot_single_subject_subject.id_feature_level_Family_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_antiexposedall_strata_delivery_Family.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_boxplot_single_subject_subject.id_feature_level_Genus_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_antiexposedall_strata_delivery_Genus.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_boxplot_single_subject_subject.id_feature_level_Genus_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_antiexposedall_strata_delivery_Genus.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_boxplot_single_subject_subject.id_feature_level_Phylum_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_antiexposedall_strata_delivery_Phylum.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_boxplot_single_subject_subject.id_feature_level_Phylum_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_antiexposedall_strata_delivery_Phylum.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0_abund_filter_0_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0_abund_filter_0_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0_abund_filter_0_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0_abund_filter_0_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0_abund_filter_0_group_group_strata_sex.pdf to C:\Users\LENOVO\AppDa problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0_abund_filter_0_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0_abund_filter_0_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_long_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_taxa_Family_prev_filter_0.01_abund_filter_0.01.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_long_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_taxa_Family_prev_filter_0.01_abund_filter_0.01.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_pair_average_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_pair_average_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_pair_average_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_chang problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_pair_average_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_pair_average_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_pair_average_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_pair_average_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_pair_indiv_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_pair_indiv_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_pair_indiv_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_pair_indiv_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_pair_indiv_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_change_heatmap_pair_indiv_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_heatmap_long_average_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_heatmap_long_average_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_heatmap_long_indiv_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_heatmap_long_indiv_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_heatmap_single_subject_subject.id_time_mo problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_heatmap_single_subject_subject.id_time_month_t_level_0_group_antiexposedall_strata_delivery_feature_level_Family_prev_filter_0.01_abund_filter_1e-04.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_heatmap_single_subject_subject.id_time_month_t_level_0_group_antiexposedall_strata_delivery_feature_level_Family_prev_filter_0.01_abund_filter_1e-04.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_heatmap_single_subject_subject.id_time_month_t_level_0_group_antiexposedall_strata_delivery_feature_level_Genus_prev_filter_0.01_abund_filter_1e-04.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_heatmap_single_subject_subject.id_time_month_t_level_0_group_antiexposedall_strata_delivery_feature_level_Genus_prev_filter_0.01_abund_filter_1e-04.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_heatmap_single_subject_subject.id_time_month_t_level_0_group_antiexposedall_strata_delivery_feature_level_Phylum_prev_filter_0.01_abund_filter_1e-04.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_heatmap_single_subject_subject.id_time_month_t_level_0_group_antiexposedall_strata_delivery_feature_level_Phylum_prev_filter_0.01_abund_filter_1e-04.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_sample_body_site_strata_ problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_sample_body_site_strata_subject_race_Family.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_sample_body_site_strata_subject_race_Family.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_long_subject_subject_time_time_feature_level_Family_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex_Family.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_long_subject_subject_time_time_feature_level_Family_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex_Family.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_long_subject_subject_time_time_feature_level_Genus_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex_Genus.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_long_subject_subject_time_time_feature_level_Genus_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex_Genus.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_long_subject_subject_time_time_feature_level_Phylum_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex_Phylum.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_long_subject_subject_time_time_feature_level_Phylum_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex_Phylum.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_long_subject_subject_time_time_feature_level_Phylum_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex_Phylum.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_single_subject_subject.id_feature_level_Family_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_antiexposedall_strata_delivery_Family.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_single_subject_subject.id_feature_level_Family_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_antiexposedall_strata_delivery_Family.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_single_subject_subject.id_feature_level_Genus_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_antiexposedall_strata_delivery_Genus.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_single_subject_subject.id_feature_level_Genus_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_antiexposedall_strata_delivery_Genus.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_single_subject_subject.id_feature_level_Phylum_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_antiexposedall_strata_delivery_Phylum.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_boxplot_single_subject_subject.id_feature_level_Phylum_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_antiexposedall_strata_delivery_Phylum.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_spaghettiplot_long_subject_subject_ problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_spaghettiplot_long_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01_base_size_16_theme_choice_bw_pdf_wid_11_pdf_hei_8.5.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_indiv_spaghettiplot_long_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01_base_size_16_theme_choice_bw_pdf_wid_11_pdf_hei_8.5.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_spaghettiplot_long_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01_base_size_16_theme_choice_bw_pdf_wid_11_pdf_hei_8.5.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpgnKPpA\Rbuildb4246c0e7f9b\cafferychen777-MicrobiomeStat-0ccb605\docs\reference\taxa_spaghettiplot_long_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01_base_size_16_theme_choice_bw_pdf_wid_11_pdf_hei_8.5.pdf: No such file or directory
ERROR
copying to build directory failed
Error: Failed to install 'MicrobiomeStat' from GitHub:
! System command 'Rcmd.exe' failed

Installation Steps
devtools::install_github("cafferychen777/MicrobiomeStat")

Environment Information:

• Operating System: Windows 11 Home
• R Version: 4.4.1
• Other Relevant Software Versions:

Attempted Solutions
I tried setting build_vignettes to TRUE, disabled OneDrive all failed.

Someone said it might be due to a registry key (r-lib/devtools#2315 (comment)), but I don't have that. Not sure how to solve this issue.

[cafferychen777]

Hi @chongchunwie,

Thank you for reporting this issue. The error appears to be related to file path/permission issues during package installation. Here are several solutions you can try:

1. Install without building vignettes:

devtools::install_github("cafferychen777/MicrobiomeStat", build_vignettes = FALSE)

2. Force installation:

devtools::install_github("cafferychen777/MicrobiomeStat", force = TRUE)

3. Clean R temporary directory before installation:

unlink(tempdir(), recursive = TRUE)
devtools::install_github("cafferychen777/MicrobiomeStat")

If the above solutions don't work, please try:

1. Run R/RStudio as administrator
2. Ensure you have the latest version of Rtools installed
3. Check if any antivirus software is blocking file operations
4. Consider installing to a shorter path location

The error is likely caused by one of these issues:

• File path length limitations in Windows
• Insufficient permissions
• PDF documentation build issues

Please let me know if any of these solutions work for you. If not, we can explore other options.

Best,
Chen

[chongchunwie]

Hi, I have tried and none of the suggestions is working.

I have also installed R 4.4.2 and set the libPaths to a shorter path location ("c:\Rlib") but it doesn't work also. I got the same error

── R CMD build ─────────────────────────────────────────────────────────────────

checking for file 'C:\Users\LENOVO\AppData\Local\Temp\RtmpiMsO9I\remotes9e941c859f\cafferychen777-MicrobiomeStat-7c77737/DESCRIPTION' ...

checking for file 'C:\Users\LENOVO\AppData\Local\Temp\RtmpiMsO9I\remotes9e941c859f\cafferychen777-MicrobiomeStat-7c77737/DESCRIPTION' ...

✔ checking for file 'C:\Users\LENOVO\AppData\Local\Temp\RtmpiMsO9I\remotes9e941c859f\cafferychen777-MicrobiomeStat-7c77737/DESCRIPTION' (412ms)

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_areaplot_pair_subject_subject_id_time_visit_number_num_feature_level_Family_feature_number_20_group_sample_body_site_strata_subject_race_avergae.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_areaplot_pair_subject_subject_id_time_visit_number_num_feature_level_Family_feature_number_20_group_sample_body_site_strata_subject_race_avergae.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_barplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_feature_number_20_group_sample_body_site_strata_subject_race_avergae.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_barplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_feature_number_20_group_sample_body_site_strata_subject_race_avergae.pdf: No such file or directory

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_boxplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_sample_body_site_strata_subject_race_Family.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_boxplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_sample_body_site_strata_subject_race_Family.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_boxplot_single_subject_subject.id_feature_level_Family_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_antiexposedall_strata_delivery_Family.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_boxplot_single_subject_subject.id_feature_level_Family_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_antiexposedall_strata_delivery_Family.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_boxplot_single_subject_subject.id_feature_level_Genus_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_antiexposedall_strata_delivery_Genus.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_boxplot_single_subject_subject.id_feature_level_Genus_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_antiexposedall_strata_delivery_Genus.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_boxplot_single_subject_subject.id_fe

 problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_boxplot_single_subject_subject.id_feature_level_Phylum_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_antiexposedall_strata_delivery_Phylum.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_boxplot_single_subject_subject.id_feature_level_Phylum_transform_sqrt_prev_filter_0.05_abund_filter_0.01_group_antiexposedall_strata_delivery_Phylum.pdf: No such file or directory

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0_abund_filter_0_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0_abund_filter_0_group_group_strata_sex.pdf: No such file or directory

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0_abund_filter_0_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0_abund_filter_0_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_long_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_taxa_Family_prev_filter_0.01_abund_filter_0.01.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_long_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_taxa_Family_prev_filter_0.01_abund_filter_0.01.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_average_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_average_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_average_subject_subject

 problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_average_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_average_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_average_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_average_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_indiv_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_indiv_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_indiv_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferyche

 problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_indiv_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_indiv_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :

 problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_indiv_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_change_heatmap_pair_indiv_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_heatmap_long_average_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_heatmap_long_average_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_heatmap_long_indiv_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_heatmap_long_indiv_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01.pdf: No such file or directory

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_heatmap_single_subject_subject.id_time_month_t_level_0_group_antiexposedall_strata_delivery_feature_level_Family_prev_filter_0.01_abund_filter_1e-04.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_heatmap_single_subject_subject.id_time_month_t_level_0_group_antiexposedall_strata_delivery_feature_level_Family_prev_filter_0.01_abund_filter_1e-04.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_heatmap_single_subject_subject.id_time_month_t_level_0_group_antiexposedall_strata_delivery_feature_level_Genus_prev_filter_0.01_abund_filter_1e-04.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_heatmap_single_subject_subject.id_time_month_t_level_0_group_antiexposedall_strata_delivery_feature_level_Genus_prev_filter_0.01_abund_filter_1e-04.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_heatmap_single_subject_subject.id_time_month_t_level_0_group_antiexposedall_strata_delivery_feature_level_Phylum_prev_filter_0.01_abund_filter_1e-04.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_heatmap_single_subject_subject.id_time_month_t_level_0_group_antiexposedall_strata_delivery_feature_level_Phylum_prev_filter_0.01_abund_filter_1e-04.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_trans

 problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_sample_body_site_strata_subject_race_Family.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_long_subject_subject_id_time_visit_number_num_feature_level_Family_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_sample_body_site_strata_subject_race_Family.pdf: No such file or directory

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_long_subject_subject_time_time_feature_level_Family_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex_Family.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_long_subject_subject_time_time_feature_level_Family_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex_Family.pdf: No such file or directory

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_long_subject_subject_time_time_feature_level_Genus_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex_Genus.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_long_subject_subject_time_time_feature_level_Genus_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex_Genus.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_long_subject_subject_time_time_feature_level_Phylum_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex_Phylum.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_long_subject_subject_time_time_feature_level_Phylum_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex_Phylum.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_single_subject_subject.id_feature_level_Family_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_antiexposedall_strata_delivery_Family.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_single_subject_subject.id_feature_level_Family_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_antiexposedall_strata_delivery_Family.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_s

 problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_single_subject_subject.id_feature_level_Genus_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_antiexposedall_strata_delivery_Genus.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_single_subject_subject.id_feature_level_Genus_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_antiexposedall_strata_delivery_Genus.pdf: No such file or directory

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_single_subject_subject.id_feature_level_Phylum_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_antiexposedall_strata_delivery_Phylum.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_boxplot_single_subject_subject.id_feature_level_Phylum_transform_sqrt_prev_filter_0.01_abund_filter_0.01_group_antiexposedall_strata_delivery_Phylum.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Family_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\

 problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Genus_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory

Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_change_boxplot_pair_subject_subject_time_time_change_base_1_feature_level_Phylum_prev_filter_0.01_abund_filter_0.01_group_group_strata_sex.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_spaghettiplot_long_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01_base_size_16_theme_choice_bw_pdf_wid_11_pdf_hei_8.5.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_indiv_spaghettiplot_long_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01_base_size_16_theme_choice_bw_pdf_wid_11_pdf_hei_8.5.pdf: No such file or directory
Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_spaghettiplot_long_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01_base_size_16_theme_choice_bw_pdf_wid_11_pdf_hei_8.5.pd

 problem copying .\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_spaghettiplot_long_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01_base_size_16_theme_choice_bw_pdf_wid_11_pdf_hei_8.5.pdf to C:\Users\LENOVO\AppData\Local\Temp\RtmpW0pQ0E\Rbuild9344348552c\cafferychen777-MicrobiomeStat-7c77737\docs\reference\taxa_spaghettiplot_long_subject_subject_id_time_visit_number_num_group_sample_body_site_strata_subject_race_feature_level_Family_prev_filter_0.01_abund_filter_0.01_base_size_16_theme_choice_bw_pdf_wid_11_pdf_hei_8.5.pdf: No such file or directory




ERROR

copying to build directory failed

Error: Failed to install 'MicrobiomeStat' from GitHub:
! System command 'Rcmd.exe' failed

[chongchunwie]

I think I solved my problem. I am able to install it after downloading the .gz file into the local drive.

[basgw]

Experiencing the same problem

[cafferychen777]

Hi @basgw,

If you're encountering the "System command 'Rcmd.exe' failed" error or issues with file path lengths during installation, here are several solutions you can try:

Solution 1: Using pak Package

The pak package often handles Windows-specific installation issues better:

if (!requireNamespace("pak", quietly = TRUE)) {
  install.packages("pak")
}
pak::pkg_install("cafferychen777/MicrobiomeStat", dependencies = TRUE)

Solution 2: Using Temporary Directory with Shorter Path

Windows has path length limitations that can cause installation issues. Here's how to work around it:

# Set temporary directory to a shorter path
dir.create("C:/Rtemp", showWarnings = FALSE)
Sys.setenv(TMPDIR = "C:/Rtemp")

# Install the package
devtools::install_github("cafferychen777/MicrobiomeStat", build_vignettes = FALSE)

Solution 3: Modify Windows Path Length Limit

1. Open PowerShell as Administrator
2. Run this command:

Set-ItemProperty -Path "HKLM:\SYSTEM\CurrentControlSet\Control\FileSystem" -Name "LongPathsEnabled" -Value 1

3. Restart your computer

Troubleshooting Steps

If you're still experiencing issues, please check:

1. Your temporary directory path:

Sys.getenv("TMPDIR")

2. Your R working directory:

getwd()

3. Make sure you have the latest version of Rtools installed for your R version

4. Try running R/RStudio as administrator

Still Having Issues?

If none of these solutions work, please provide:

• The output of Sys.getenv("TMPDIR")
• Your R working directory (getwd())
• Complete error message
• Your R version (R.version)

This will help us provide more targeted assistance for your specific setup.

Best,
Chen