* installing *source* package ‘birp’ ...
** this is package ‘birp’ version ‘0.0.6’
** package ‘birp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/bin/sh: !!!: command not found
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying 104.192.143.23:443...
* Connected to bitbucket.org (104.192.143.23) port 443 (#0)
* ALPN: offers h2
* ALPN: offers http/1.1
* [CONN-0-0][CF-SSL] (304) (OUT), TLS handshake, Client hello (1):
} [318 bytes data]
* [CONN-0-0][CF-SSL] (304) (IN), TLS handshake, Server hello (2):
{ [122 bytes data]
* [CONN-0-0][CF-SSL] (304) (IN), TLS handshake, Unknown (8):
{ [15 bytes data]
* [CONN-0-0][CF-SSL] (304) (IN), TLS handshake, Certificate (11):
{ [2816 bytes data]
* [CONN-0-0][CF-SSL] (304) (IN), TLS handshake, CERT verify (15):
{ [79 bytes data]
* [CONN-0-0][CF-SSL] (304) (IN), TLS handshake, Finished (20):
{ [52 bytes data]
* [CONN-0-0][CF-SSL] (304) (OUT), TLS handshake, Finished (20):
} [52 bytes data]
* SSL connection using TLSv1.3 / AEAD-AES256-GCM-SHA384
* ALPN: server accepted h2
* Server certificate:
* subject: CN=*.bitbucket.org
* start date: Jun 9 00:00:00 2026 GMT
* expire date: Dec 23 23:59:59 2026 GMT
* issuer: C=US; O=Amazon; CN=Amazon ECDSA 256 M04
* SSL certificate verify ok.
* Using HTTP2, server supports multiplexing
* Copying HTTP/2 data in stream buffer to connection buffer after upgrade: len=0
* h2h3 [:method: GET]
* h2h3 [:path: /wegmannlab/birp_cpp/get/d4b998e55207919c2e0ff4a72752e92e4750fddd.tar.gz]
* h2h3 [:scheme: https]
* h2h3 [:authority: bitbucket.org]
* h2h3 [user-agent: curl/7.87.0]
* h2h3 [accept: */*]
* Using Stream ID: 1 (easy handle 0x7f9f76014000)
> GET /wegmannlab/birp_cpp/get/d4b998e55207919c2e0ff4a72752e92e4750fddd.tar.gz HTTP/2
> Host: bitbucket.org
> user-agent: curl/7.87.0
> accept: */*
>
* Connection state changed (MAX_CONCURRENT_STREAMS == 64)!
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0< HTTP/2 200
< date: Sat, 22 Aug 2026 11:34:34 GMT
< content-type: application/x-tar-gz; charset=utf-8
< content-length: 57516
< server: AtlassianEdge
< expires: Sat, 22 Aug 2026 11:34:34 GMT
< cache-control: max-age=0, no-cache, no-store, must-revalidate, private
< content-disposition: attachment; filename=wegmannlab-birp_cpp-d4b998e55207.tar.gz
< x-content-type-options: nosniff
< x-xss-protection: 1; mode=block
< atl-traceid: 0512fce93d4b41bdbc37da55820af97b
< atl-request-id: 0512fce9-3d4b-41bd-bc37-da55820af97b
< strict-transport-security: max-age=63072000; includeSubDomains; preload
< report-to: {"endpoints": [{"url": "https://dz8aopenkvv6s.cloudfront.net"}], "group": "endpoint-1", "include_subdomains": true, "max_age": 600}
< nel: {"failure_fraction": 0.01, "include_subdomains": true, "max_age": 600, "report_to": "endpoint-1"}
< x-ratelimit-limit: 5000, 5000;w=60
< x-ratelimit-remaining: 4999
< x-ratelimit-reset: 27
< server-timing: atl-edge;dur=955,atl-edge-internal;dur=8,atl-edge-upstream;dur=948,atl-edge-pop;desc="aws-ap-southeast-2"
<
{ [15673 bytes data]
100 57516 100 57516 0 0 39474 0 0:00:01 0:00:01 --:--:-- 39638
* Connection #0 to host bitbucket.org left intact
x wegmannlab-birp_cpp-d4b998e55207/
x wegmannlab-birp_cpp-d4b998e55207/.gitignore
x wegmannlab-birp_cpp-d4b998e55207/CMakeLists.txt
x wegmannlab-birp_cpp-d4b998e55207/LICENSE
x wegmannlab-birp_cpp-d4b998e55207/README.MD
x wegmannlab-birp_cpp-d4b998e55207/compile_birp.sh
x wegmannlab-birp_cpp-d4b998e55207/core/
x wegmannlab-birp_cpp-d4b998e55207/core/BirpDAG.h
x wegmannlab-birp_cpp-d4b998e55207/core/BirpTypes.h
x wegmannlab-birp_cpp-d4b998e55207/core/TBirpConfiguration.cpp
x wegmannlab-birp_cpp-d4b998e55207/core/TBirpConfiguration.h
x wegmannlab-birp_cpp-d4b998e55207/core/TBirpCore.cpp
x wegmannlab-birp_cpp-d4b998e55207/core/TBirpCore.h
x wegmannlab-birp_cpp-d4b998e55207/core/TBirpPrior.cpp
x wegmannlab-birp_cpp-d4b998e55207/core/TBirpPrior.h
x wegmannlab-birp_cpp-d4b998e55207/core/TBirpTask.cpp
x wegmannlab-birp_cpp-d4b998e55207/core/TBirpTask.h
x wegmannlab-birp_cpp-d4b998e55207/core/TData.cpp
x wegmannlab-birp_cpp-d4b998e55207/core/TData.h
x wegmannlab-birp_cpp-d4b998e55207/core/TDistributions.cpp
x wegmannlab-birp_cpp-d4b998e55207/core/TDistributions.h
x wegmannlab-birp_cpp-d4b998e55207/core/TGamma.cpp
x wegmannlab-birp_cpp-d4b998e55207/core/TGamma.h
x wegmannlab-birp_cpp-d4b998e55207/core/TModels.cpp
x wegmannlab-birp_cpp-d4b998e55207/core/TModels.h
x wegmannlab-birp_cpp-d4b998e55207/core/TUniqueContainer.h
x wegmannlab-birp_cpp-d4b998e55207/main.cpp
x wegmannlab-birp_cpp-d4b998e55207/tests/
x wegmannlab-birp_cpp-d4b998e55207/tests/.gitignore
x wegmannlab-birp_cpp-d4b998e55207/tests/birp_regressionTests
x wegmannlab-birp_cpp-d4b998e55207/tests/find_birp
x wegmannlab-birp_cpp-d4b998e55207/tests/workflow.test
/bin/sh: -S: command not found
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Ibirp_cpp/coretools/core/ -Ibirp_cpp/coretools/fast_float/include/ -Ibirp_cpp/coretools/arma/include/ -Ibirp_cpp/stattools/core/ -Ibirp_cpp/core/ -DUSE_RCPP -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Ibirp_cpp/coretools/core/ -Ibirp_cpp/coretools/fast_float/include/ -Ibirp_cpp/coretools/arma/include/ -Ibirp_cpp/stattools/core/ -Ibirp_cpp/core/ -DUSE_RCPP -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o
In file included from main.cpp:2:
birp_cpp/core/TBirpTask.h:4:10: fatal error: 'coretools/Main/TTask.h' file not found
#include "coretools/Main/TTask.h"
^~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [main.o] Error 1
make: *** Waiting for unfinished jobs....
ERROR: compilation failed for package ‘birp’
* removing ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/birp.Rcheck/birp’